Variant report

Variant	rs9311439
Chromosome Location	chr3:49310408-49310409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10049462	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10154895	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10865954	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11130184	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1134043	0.90[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11710247	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11715581	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11716445	0.89[CEU][hapmap]
rs11718982	0.81[EUR][1000 genomes]
rs11719220	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11720460	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11920267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12490393	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12493001	1.00[JPT][hapmap]
rs12493284	0.89[ASN][1000 genomes]
rs12629637	0.92[ASN][1000 genomes]
rs12629759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12631989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12637576	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12715434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13064780	0.81[ASN][1000 genomes]
rs13068038	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13077498	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13096406	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2117938	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2304442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3212	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs34326553	0.82[EUR][1000 genomes]
rs34343820	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34580506	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs34784192	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35060561	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35174559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs35185152	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35218722	0.81[ASN][1000 genomes]
rs35283189	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs35673421	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3774799	0.81[ASN][1000 genomes]
rs4279134	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4410472	0.86[ASN][1000 genomes]
rs4513485	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4521268	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4955410	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4955418	1.00[JPT][hapmap]
rs4955419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4955420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4955432	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5030795	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs56306491	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66991555	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67286839	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6779394	1.00[JPT][hapmap]
rs67831908	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6784111	1.00[JPT][hapmap]
rs71324939	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73084135	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7374375	0.82[ASN][1000 genomes]
rs7614738	0.88[ASN][1000 genomes]
rs7626445	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7638154	0.92[ASN][1000 genomes]
rs7652746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9814987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9826525	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9828310	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9835439	0.87[EUR][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9840050	0.82[CHB][hapmap]
rs9844757	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9847839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9850917	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855123	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9862483	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9870030	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9874474	0.92[ASN][1000 genomes]
rs9880088	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883409	0.92[ASN][1000 genomes]
rs9990153	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv963481	chr3:49304260-49325571	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9311439	WDR6	cis	Artery Tibial	GTEx
rs9311439	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9311439	WDR6	cis	Esophagus Mucosa	GTEx
rs9311439	WDR6	cis	Adipose Subcutaneous	GTEx
rs9311439	WDR6	cis	Whole Blood	GTEx
rs9311439	USP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49286400-49313600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:49293000-49313400	Weak transcription	HSMM	muscle
3	chr3:49294800-49313400	Weak transcription	NHLF	lung
4	chr3:49295000-49313200	Weak transcription	Right Ventricle	heart
5	chr3:49299000-49313600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:49300200-49313400	Weak transcription	HUVEC	blood vessel
7	chr3:49301800-49315600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49302200-49311800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:49302800-49313400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:49303600-49315600	Weak transcription	HepG2	liver
11	chr3:49304200-49313200	Weak transcription	Brain Germinal Matrix	brain
12	chr3:49304200-49313400	Weak transcription	NHDF-Ad	bronchial
13	chr3:49304400-49313200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:49304400-49313400	Weak transcription	Fetal Kidney	kidney
15	chr3:49304400-49313400	Weak transcription	Stomach Mucosa	stomach
16	chr3:49304400-49313600	Weak transcription	Fetal Brain Male	brain
17	chr3:49304800-49311600	Strong transcription	Fetal Stomach	stomach
18	chr3:49304800-49313200	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:49304800-49313200	Weak transcription	Left Ventricle	heart
20	chr3:49304800-49313400	Weak transcription	Osteobl	bone
21	chr3:49304800-49313600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:49304800-49313600	Weak transcription	Liver	Liver
23	chr3:49304800-49314000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:49305000-49312600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:49305000-49313200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:49305000-49313200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:49305000-49313400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:49305000-49313400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:49305000-49313400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:49305000-49313400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:49305000-49313400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:49305000-49313400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:49305000-49313600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:49305000-49313600	Weak transcription	Brain Substantia Nigra	brain
35	chr3:49305200-49311400	Weak transcription	K562	blood
36	chr3:49305200-49313400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:49305400-49313600	Weak transcription	NHEK	skin
38	chr3:49305600-49313200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:49305600-49313200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:49305800-49313200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:49305800-49313600	Weak transcription	Colonic Mucosa	Colon
42	chr3:49306200-49310800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:49306200-49313400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:49306400-49311000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr3:49306600-49310800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:49306600-49311600	Strong transcription	Fetal Muscle Leg	muscle
47	chr3:49307000-49313200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:49307000-49313200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:49307000-49313400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:49307200-49313200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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