TGN - INAVA

View Mode Credible Sets LD Summary (0.6 r2 threshold, 1KGp3:EUR) Hide non-coding genes

Summary (INAVA TSS Ensembl 90:chr1:200,894,821)

Association Results

Display Name	Phenotype	Source	Year	Index Variant	Allele	Pvalue	OR/Beta	Curator Comment
Schizophrenia 2.90e-08 1.05 C	Schizophrenia	daner_PGC_SCZ_w3_90_0418b.gz.p4.clump.areator.sorted.1mhc.xls; PGC Schizophrenia 3	2018	rs12126806	C	2.90e-08	1.05
Inflammatory bowel disease 1.00e-21	Inflammatory bowel disease	de Lange KM; Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease.	2017	rs7554511		1.00e-21
Crohn's disease (time to surgery) 1.00e-10	Crohn's disease (time to surgery)	de Lange KM; Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease.	2017	rs7554511		1.00e-10
Ulcerative colitis 4.00e-16	Ulcerative colitis	de Lange KM; Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease.	2017	rs7554511		4.00e-16
Non-cancer illness code, self-reported: hypothyroidism/myxoedema 1.21e-07 0.00 C	Non-cancer illness code, self-reported: hypothyroidism/myxoedema	UK Biobank Rapid GWAS	2017	rs12756886	C Audited	1.21e-07	0.00	variant: 1:200840467:T:C; nCompleteSamples: 337159; AC: 8.18581e+04; ytx: 4.28891e+03; se: 7.96361e-04; tstat: 5.29280e+00;
Home area population density - urban or rural: Postcode not linkable 4.05e-07 0.00 A	Home area population density - urban or rural: Postcode not linkable	UK Biobank Rapid GWAS	2017	rs115600509	A Audited	4.05e-07	0.00	variant: 1:200866151:G:A; nCompleteSamples: 333997; AC: 1.47883e+04; ytx: 3.94510e+00; se: 5.34676e-05; tstat: 5.06692e+00;
Impedance of whole body 3.94e-08 0.02 A	Impedance of whole body	UK Biobank Rapid GWAS	2017	rs71635524	A Audited	3.94e-08	0.02	variant: 1:200893960:G:A; nCompleteSamples: 331284; AC: 3.72655e+04; ytx: 1.43264e+02; se: 4.14650e-03; tstat: 5.49345e+00;
Impedance of arm (right) 1.57e-11 0.03 A	Impedance of arm (right)	UK Biobank Rapid GWAS	2017	rs71635524	A Audited	1.57e-11	0.03	variant: 1:200893960:G:A; nCompleteSamples: 331279; AC: 3.72668e+04; ytx: 8.98302e+01; se: 3.82389e-03; tstat: 6.74188e+00;
Impedance of arm (left) 5.65e-12 0.03 A	Impedance of arm (left)	UK Biobank Rapid GWAS	2017	rs71635524	A Audited	5.65e-12	0.03	variant: 1:200893960:G:A; nCompleteSamples: 331292; AC: 3.72674e+04; ytx: 2.36164e+02; se: 3.84016e-03; tstat: 6.88844e+00;
Arm fat-free mass (right) 7.62e-08 -0.02 A	Arm fat-free mass (right)	UK Biobank Rapid GWAS	2017	rs71635524	A Audited	7.62e-08	-0.02	variant: 1:200893960:G:A; nCompleteSamples: 331221; AC: 3.72601e+04; ytx: 4.93474e+02; se: 3.38829e-03; tstat: -5.37607e+00;
Arm predicted mass (right) 7.90e-07 -0.02 A	Arm predicted mass (right)	UK Biobank Rapid GWAS	2017	rs71635524	A Audited	7.90e-07	-0.02	variant: 1:200893960:G:A; nCompleteSamples: 331216; AC: 3.72593e+04; ytx: 5.48381e+02; se: 3.37629e-03; tstat: -4.93781e+00;
Arm fat-free mass (left) 1.15e-07 -0.02 A	Arm fat-free mass (left)	UK Biobank Rapid GWAS	2017	rs71635524	A Audited	1.15e-07	-0.02	variant: 1:200893960:G:A; nCompleteSamples: 331159; AC: 3.72523e+04; ytx: 4.17489e+02; se: 3.45713e-03; tstat: -5.30199e+00;
Arm predicted mass (left) 3.63e-07 -0.02 A	Arm predicted mass (left)	UK Biobank Rapid GWAS	2017	rs71635524	A Audited	3.63e-07	-0.02	variant: 1:200893960:G:A; nCompleteSamples: 331146; AC: 3.72503e+04; ytx: 4.37866e+02; se: 3.44425e-03; tstat: -5.08742e+00;
Trunk fat-free mass 7.17e-08 -0.02 A	Trunk fat-free mass	UK Biobank Rapid GWAS	2017	rs71635524	A Audited	7.17e-08	-0.02	variant: 1:200893960:G:A; nCompleteSamples: 331030; AC: 3.72418e+04; ytx: 5.66293e+02; se: 3.42503e-03; tstat: -5.38706e+00;
Trunk predicted mass 9.66e-08 -0.02 A	Trunk predicted mass	UK Biobank Rapid GWAS	2017	rs71635524	A Audited	9.66e-08	-0.02	variant: 1:200893960:G:A; nCompleteSamples: 330995; AC: 3.72406e+04; ytx: 5.63911e+02; se: 3.41377e-03; tstat: -5.33310e+00;
Underlying (primary) cause of death: ICD10: C14.0 Pharynx, unspecified 6.26e-07 0.01 G	Underlying (primary) cause of death: ICD10: C14.0 Pharynx, unspecified	UK Biobank Rapid GWAS	2017	rs61825264	G	6.26e-07	0.01	variant: 1:200853330:C:G; nCompleteSamples: 7637; AC: 3.37267e+02; ytx: 3.00392e+00; se: 1.69853e-03; tstat: 4.98717e+00;
Underlying (primary) cause of death: ICD10: D43.2 Brain, unspecified 4.52e-07 0.01 A	Underlying (primary) cause of death: ICD10: D43.2 Brain, unspecified	UK Biobank Rapid GWAS	2017	rs55637677	A Audited	4.52e-07	0.01	variant: 1:200920763:G:A; nCompleteSamples: 7637; AC: 2.10502e+02; ytx: 2.87059e+00; se: 2.53880e-03; tstat: 5.04987e+00;
Underlying (primary) cause of death: ICD10: I38 Endocarditis, valve unspecified 1.62e-14 0.02 T	Underlying (primary) cause of death: ICD10: I38 Endocarditis, valve unspecified	UK Biobank Rapid GWAS	2017	rs566470356	T Audited	1.62e-14	0.02	variant: 1:200913519:G:T; nCompleteSamples: 7637; AC: 1.36012e+02; ytx: 2.98039e+00; se: 2.81435e-03; tstat: 7.69254e+00;
Underlying (primary) cause of death: ICD10: I60.7 Subarachnoid haemorrhage from intracranial artery, unspecified 2.67e-08 0.01 C	Underlying (primary) cause of death: ICD10: I60.7 Subarachnoid haemorrhage from intracranial artery, unspecified	UK Biobank Rapid GWAS	2017	rs140787791	C Audited	2.67e-08	0.01	variant: 1:200833522:T:C; nCompleteSamples: 7637; AC: 1.29435e+02; ytx: 2.00000e+00; se: 2.66198e-03; tstat: 5.56745e+00;
Inflammatory bowel disease 8.00e-45	Inflammatory bowel disease	Liu JZ; Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.	2015	rs35730213		8.00e-45
Crohn's disease (time to surgery) 2.00e-27 1.16 A	Crohn's disease (time to surgery)	Liu JZ; Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.	2015	rs7554511	A	2.00e-27	1.16
Ulcerative colitis 7.00e-31 1.18 C	Ulcerative colitis	Liu JZ; Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.	2015	rs7554511	C	7.00e-31	1.18
Ulcerative colitis 5.00e-06 1.41	Ulcerative colitis	Julià A; A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis.	2014	rs7554511		5.00e-06	1.41
Epilepsy 1.00e-08 1.59	Epilepsy	Guo Y; Two-stage genome-wide association study identifies variants in CAMSAP1L1 as susceptibility loci for epilepsy in Chinese.	2012	rs2292096		1.00e-08	1.59
Inflammatory bowel disease 1.00e-32 1.16 C	Inflammatory bowel disease	Jostins L; Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.	2012	rs7554511	C	1.00e-32	1.16
Multiple sclerosis 2.00e-09 1.11 G	Multiple sclerosis	International Multiple Sclerosis Genetics Consortium; Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.	2011	rs7522462	G	2.00e-09	1.11
Ulcerative colitis 2.00e-13 1.19 C	Ulcerative colitis	Anderson CA; Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.	2011	rs7554511	C	2.00e-13	1.19
CELIAC DISEASE 4.00e-09 1.12	CELIAC DISEASE	Dubois PC; Multiple common variants for celiac disease influencing immune gene expression.	2010	rs296547		4.00e-09	1.12
Crohn's disease (time to surgery) 2.00e-07 1.14 C	Crohn's disease (time to surgery)	Franke A; Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.	2010	rs7554511	C	2.00e-07	1.14
Ulcerative colitis 1.00e-06	Ulcerative colitis	UK IBD Genetics Consortium; Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.	2009	rs7554511		1.00e-06

Association Details

1st Author	Year	Journal/Site/File	Title/Description

pQTL Results

Display Name	Phenotype	Source	Year	Index Variant	Allele	Pvalue	OR/Beta	Credible Set	Show	Curator Comment

pQTL Details

1st Author	Year	Journal/Site/File	Title/Description

eQTL Results

Display Name	Tissue	Gene	Source	Year	Index Variant	Pvalue	Beta	Curator Comment
EQTL GTeX MROH3P Skin Sun Exposed Lower leg 6.24e-10	Skin Sun Exposed Lower leg	MROH3P	GTEx Consortium	2015	rs296521	6.24e-10	-0.36	Tissue pval threshold = 1.34e-05	0
EQTL GTeX INAVA Artery Tibial 5.62e-12	Artery Tibial	INAVA	GTEx Consortium	2015	rs296539	5.62e-12	0.44	Tissue pval threshold = 1.37e-05	1
EQTL GTeX MROH3P Artery Tibial 4.69e-29	Artery Tibial	MROH3P	GTEx Consortium	2015	rs296547	4.69e-29	0.71	Tissue pval threshold = 1.43e-05	1
EQTL GTeX INAVA Skin Sun Exposed Lower leg 1.05e-05	Skin Sun Exposed Lower leg	INAVA	GTEx Consortium	2015	rs296556	1.05e-05	-0.19	Tissue pval threshold = 1.38e-05	0
EQTL GTeX INAVA Artery Aorta 7.49e-06	Artery Aorta	INAVA	GTEx Consortium	2015	rs169850	7.49e-06	0.32	Tissue pval threshold = 1.51e-05	2
EQTL GTeX CAMSAP2 Cells Transformed fibroblasts 1.04e-06	Cells Transformed fibroblasts	CAMSAP2	GTEx Consortium	2015	rs296533	1.04e-06	-0.12	Tissue pval threshold = 1.11e-05	4
EQTL GTeX INAVA Esophagus Mucosa 1.81e-11	Esophagus Mucosa	INAVA	GTEx Consortium	2015	rs10800746	1.81e-11	0.33	Tissue pval threshold = 1.41e-05	2
EQTL GTeX MROH3P Esophagus Mucosa 1.83e-09	Esophagus Mucosa	MROH3P	GTEx Consortium	2015	rs296521	1.83e-09	-0.44	Tissue pval threshold = 1.70e-05	0
EQTL GTeX MROH3P Skin Sun Exposed Lower leg 1.20e-05	Skin Sun Exposed Lower leg	MROH3P	GTEx Consortium	2015	rs7531238	1.20e-05	0.24	Tissue pval threshold = 1.34e-05	0
EQTL GTeX MROH3P Artery Aorta 1.72e-14	Artery Aorta	MROH3P	GTEx Consortium	2015	rs905634	1.72e-14	-0.67	Tissue pval threshold = 1.31e-05	2
EQTL GTeX INAVA Skin Sun Exposed Lower leg 3.71e-17	Skin Sun Exposed Lower leg	INAVA	GTEx Consortium	2015	rs296520	3.71e-17	-0.27	Tissue pval threshold = 1.38e-05	6
EQTL GTeX CAMSAP2 Testis 2.06e-06	Testis	CAMSAP2	GTEx Consortium	2015	rs10920052	2.06e-06	-0.38	Tissue pval threshold = 1.62e-05	0
EQTL GTeX CAMSAP2 Muscle Skeletal 6.10e-06	Muscle Skeletal	CAMSAP2	GTEx Consortium	2015	rs79263210	6.10e-06	-0.25	Tissue pval threshold = 7.63e-06	0
EQTL GTeX MROH3P Artery Coronary 1.26e-11	Artery Coronary	MROH3P	GTEx Consortium	2015	rs905634	1.26e-11	-0.80	Tissue pval threshold = 4.38e-06	2
EQTL GTeX INAVA Skin Not Sun Exposed Suprapubic 2.36e-15	Skin Not Sun Exposed Suprapubic	INAVA	GTEx Consortium	2015	rs7522462	2.36e-15	0.43	Tissue pval threshold = 7.30e-06	6

Variants of Interest

Name	Non-Reference Allele	Location	Gene	Protein Change	Polyphen	f(NFE)	f(Max)
rs139334989	T	200,847,220	CAMSAP2	p.Ala385Ser	benign	0.000	0.002
rs147502751	T	200,847,244	CAMSAP2	p.His393Tyr	benign	0.000	0.002
rs553031275	C	200,848,111	CAMSAP2	p.Ile459Leu	benign	0.000	0.001
rs147174162	G	200,848,130	CAMSAP2	p.Asn465Ser	benign	0.000	0.011
rs57213993	G	200,848,157	CAMSAP2	p.His474Arg	benign	0.000	0.009
rs60174212	A	200,848,271	CAMSAP2	p.Cys512Tyr	benign	0.000	0.009
rs766122905	C	200,848,309	CAMSAP2	p.Asn525His	benign	0.000	0.001
rs34958390	C	200,848,637	CAMSAP2	p.Met634Thr	benign	0.001	0.007
rs147411465	A	200,848,870	CAMSAP2	p.Asp712Asn	possibly damaging	0.000	0.007
rs145940629	G	200,849,279	CAMSAP2	p.Ile848Arg	benign	0.001	0.007
rs189038502	G	200,849,335	CAMSAP2	p.Ile867Val	benign	0.000	0.001
rs573116116	G	200,849,408	CAMSAP2	p.Tyr891Cys	benign	0.000	0.001
rs905226210	T	200,849,636	CAMSAP2	p.Thr967Ile	benign	0.000	0.001
rs3753952	T	200,849,642	CAMSAP2	p.Pro969Leu	benign	0.000	0.001
rs145337502	T	200,849,699	CAMSAP2	p.Thr988Ile	benign	0.000	0.003
rs201133949	T	200,849,851	CAMSAP2	p.Pro1039Ser	benign	0.000	0.003
rs6674599	G	200,849,852	CAMSAP2	p.Pro1039Arg	benign	0.011	0.012
rs767979653	G	200,849,996	CAMSAP2	p.Pro1087Arg	benign	0.000	0.001
rs150711965	G	200,850,101	CAMSAP2	p.Asn1122Ser	benign	0.002	0.002
rs147490223	A	200,853,311	CAMSAP2	p.Asp1224Glu	benign	0.000	0.010
rs199622691	T	200,853,354	CAMSAP2	p.Arg1239Trp	probably damaging	0.000	0.001
rs201345201	C	200,873,117	GPR25	p.Leu27Pro	benign	0.000	0.006
rs138176594	C	200,873,213	GPR25	p.Phe59Ser	possibly damaging	0.012	0.017
rs200195345	C	200,873,468	GPR25	p.Leu144Pro	benign	0.002	0.002
rs144298915	T	200,873,513	GPR25	p.Ser159Leu	benign	0.021	0.027
rs745766590	C	200,873,548	GPR25	p.Gly171Arg	probably damaging	0.000	0.003
rs140797590	C	200,873,999	GPR25	p.Gly321Ala	benign	0.000	0.010
rs199987519	A	200,874,084	GPR25	p.Cys349Ter		0.000	0.002
rs200080169	G	200,874,116	GPR25	p.Ser360Cys	benign	0.003	0.003
rs41269923	A	200,898,444	INAVA	p.Ile15Asn	probably damaging	0.008	0.010
rs181832255	T	200,899,545	INAVA	p.Ala43Val	benign	0.000	0.006
rs150962388	T	200,900,111	INAVA	p.Thr63Met	probably damaging	0.000	0.002
rs758954062	A	200,900,998	INAVA	p.Arg120His	benign	0.000	0.001
rs757620702	T	200,901,036	INAVA	p.Arg133Trp	probably damaging	0.000	0.001
rs369240943	A	200,901,037	INAVA	p.Arg133Gln	probably damaging	0.000	0.001
rs536183830	G	200,901,082	INAVA	p.Gln148Arg	benign	0.000	0.001
rs141815054	A	200,901,094	INAVA	p.Arg152His	benign	0.004	0.013
rs774931721	A	200,901,115	INAVA	p.Arg159His	possibly damaging	0.000	0.001
rs1025424742	C	200,907,882	INAVA	p.Glu190Ala	probably damaging	0.000	0.001
rs951181429	T	200,908,786	INAVA	p.Leu211Phe	benign	0.000	0.002
rs200620097	T	200,908,846	INAVA	p.Arg231Trp	probably damaging	0.000	0.003
rs143222538	A	200,908,849	INAVA	p.Ala232Thr	benign	0.000	0.015
rs41313912	T	200,908,898	INAVA	p.Tyr248Phe	probably damaging	0.011	0.011
rs761605707	T	200,909,385	INAVA	p.Ser316Leu	benign	0.000	0.001
rs527548422	A	200,911,467	INAVA	p.Arg325Gln	benign	0.000	0.003
rs145738054	A	200,911,554	INAVA	p.Pro354His	benign	0.000	0.009
rs61740234	T	200,911,574	INAVA	p.Pro361Ser	benign	0.009	0.143
rs116087951	G	200,911,689	INAVA	p.Ser399Cys	benign	0.000	0.011
rs45547233	C	200,911,741	INAVA	p.Arg416Ser	benign	0.122	0.164
rs772463898	A	200,911,751	INAVA	p.Ala420Thr	benign	0.000	0.001
rs296520	T	200,911,850	INAVA	p.Arg453Cys	benign	0.741	0.998
rs199499268	G	200,911,868	INAVA	p.Pro459Ala	benign	0.000	0.007
rs61745433	T	200,911,898	INAVA	p.Arg469Cys	benign	0.001	0.007
rs552392029	A	200,912,018	INAVA	p.Glu509Lys	benign	0.000	0.001
rs566211439	A	200,912,037	INAVA	p.Ser515Asn	benign	0.000	0.003
rs143834031	A	200,913,559	INAVA	p.Arg556Gln	benign	0.001	0.003
rs182875303	A	200,928,313	MROH3P			0.000	0.001

Functional Variants Details

1st Author	Year	Journal/Site/File	Title/Description

Expression Data Details

1st Author	Year	Journal/Site/File	Title/Description
GTEx Consortium	2015	Science	Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.
INAVA GTEx V7 Median Expression
CAMSAP2 GTEx V7 Median Expression
RPL34P6 GTEx V7 Median Expression
GPR25 GTEx V7 Median Expression
MROH3P GTEx V7 Median Expression
RNU6-704P GTEx V7 Median Expression

Protein and Structure Chemistry Details

1st Author	Year	Journal/Site/File	Title/Description

Clinical Results

Phenotype/Gene Associations

Phenotype	Gene	Source	Curator Comment

Phenotype/Allele Associations

Phenotype	Variant	Unaudited Risk Allele	Clinical Signficance	Transcript-Impact Genes	Source

Clinical Data Details

1st Author	Year	Journal/Site/File	Title/Description

References (13 out of 13 not yet reviewed)

Reviewed	1st Author	Year	Journal/Site/File	Title/Description
		2018	daner_PGC_SCZ_w3_90_0418b.gz.p4.clump.areator.sorted.1mhc.xls	PGC Schizophrenia 3

	de Lange KM	2017	Nat. Genet.	Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease.

		2017	http://www.nealelab.is/blog/2017/7/19/rapid-gwas-of-thousands-of-phenotypes-for-337000-samples-in-the-uk-biobank	UK Biobank Rapid GWAS

	Liu JZ	2015	Nat. Genet.	Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.

	GTEx Consortium	2015	Science	Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.
Section Assignment INAVA GTEx V7 Median Expression
Section Assignment CAMSAP2 GTEx V7 Median Expression
Section Assignment RPL34P6 GTEx V7 Median Expression
Section Assignment GPR25 GTEx V7 Median Expression
Section Assignment MROH3P GTEx V7 Median Expression
Section Assignment RNU6-704P GTEx V7 Median Expression

	Julià A	2014	Hum. Mol. Genet.	A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis.

	Guo Y	2012	Hum. Mol. Genet.	Two-stage genome-wide association study identifies variants in CAMSAP1L1 as susceptibility loci for epilepsy in Chinese.

	Jostins L	2012	Nature	Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.

	International Multiple Sclerosis Genetics Consortium	2011	Nature	Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

	Anderson CA	2011	Nat. Genet.	Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.

	Dubois PC	2010	Nat. Genet.	Multiple common variants for celiac disease influencing immune gene expression.

	Franke A	2010	Nat. Genet.	Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.

	UK IBD Genetics Consortium	2009	Nat. Genet.	Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.