Variant report

Variant	rs12629759
Chromosome Location	chr3:49237394-49237395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 38 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10049462	1.00[JPT][hapmap]
rs10154895	0.87[ASN][1000 genomes]
rs10865954	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130182	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130185	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11552724	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11706052	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11706189	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11710247	0.81[ASN][1000 genomes]
rs11712006	0.82[ASN][1000 genomes]
rs11713297	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11715581	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716334	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717524	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11719220	0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11920267	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12487580	0.87[ASN][1000 genomes]
rs12490393	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493001	0.89[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629637	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12631989	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12636030	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13064780	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13064784	0.87[ASN][1000 genomes]
rs13068038	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs13077498	1.00[JPT][hapmap]
rs13316620	0.80[CEU][hapmap]
rs2117938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2304442	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2334958	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs34326553	0.82[ASN][1000 genomes]
rs34566463	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34580506	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34889065	0.82[ASN][1000 genomes]
rs35060561	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35174559	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35218722	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35283189	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs35673421	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3774800	0.96[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs4279134	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs4308307	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4367098	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4499638	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4513485	0.84[ASW][hapmap];0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs4521268	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs4536858	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4955410	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs4955418	0.92[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4955419	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955420	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5030795	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs55713230	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61583136	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62262517	0.85[ASN][1000 genomes]
rs66991555	0.97[ASN][1000 genomes]
rs6770112	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6779394	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs6781790	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs6784111	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6790914	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6794924	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6795756	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6795772	0.91[LWK][hapmap];0.98[MKK][hapmap]
rs7432989	0.85[CEU][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs7615235	0.85[ASN][1000 genomes]
rs7626445	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs7638154	0.84[EUR][1000 genomes]
rs7652746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9311439	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9814987	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9835439	0.92[ASN][1000 genomes]
rs9837237	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9837625	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9840050	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs9846123	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs9847839	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9850917	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9855123	0.92[ASN][1000 genomes]
rs9862483	0.87[ASN][1000 genomes]
rs9880088	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9880309	1.00[JPT][hapmap]
rs9990153	0.87[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:38)

SNP	Gene	Cis/trans	Tissue	Source
rs12629759	TLR9	cis	parietal	SCAN
rs12629759	CCDC71	cis	cerebellum	SCAN
rs12629759	P4HTM	cis	cerebellum	SCAN
rs12629759	WDR6	cis	lung	GTEx
rs12629759	WDR6	cis	Whole Blood	GTEx
rs12629759	AMT	cis	Whole Blood	GTEx
rs12629759	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs12629759	WDR6	cis	Heart Left Ventricle	GTEx
rs12629759	NCKIPSD	cis	parietal	SCAN
rs12629759	CCDC36	cis	Artery Tibial	GTEx
rs12629759	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs12629759	AMT	cis	Muscle Skeletal	GTEx
rs12629759	CCDC36	cis	Esophagus Muscularis	GTEx
rs12629759	P4HTM	cis	parietal	SCAN
rs12629759	WDR6	cis	Artery Tibial	GTEx
rs12629759	SEMA3G	cis	cerebellum	SCAN
rs12629759	WDR6	cis	Adipose Subcutaneous	GTEx
rs12629759	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs12629759	WDR6	cis	Esophagus Mucosa	GTEx
rs12629759	WDR6	cis	parietal	SCAN
rs12629759	WDR6	cis	Muscle Skeletal	GTEx
rs12629759	AMT	cis	Thyroid	GTEx
rs12629759	WDR6	cis	lymphoblastoid	seeQTL
rs12629759	AMT	cis	parietal	SCAN
rs12629759	ARIH2	cis	Thyroid	GTEx
rs12629759	ZNF589	cis	parietal	SCAN
rs12629759	WDR6	cis	Nerve Tibial	GTEx
rs12629759	NCKIPSD	cis	Muscle Skeletal	GTEx
rs12629759	NICN1	cis	Thyroid	GTEx
rs12629759	WDR6	cis	Esophagus Muscularis	GTEx
rs12629759	C3orf62	cis	cerebellum	SCAN
rs12629759	NICN1-AS1	cis	Thyroid	GTEx
rs12629759	WDR6	cis	cerebellum	SCAN
rs12629759	DALRD3	cis	cerebellum	SCAN
rs12629759	CXorf38	trans	parietal	SCAN
rs12629759	AMT	cis	Artery Aorta	GTEx
rs12629759	NCKIPSD	cis	cerebellum	SCAN
rs12629759	AMT	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49235800-49237600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:49236000-49238400	Enhancers	Fetal Heart	heart
3	chr3:49236200-49237800	Flanking Active TSS	Fetal Muscle Leg	muscle
4	chr3:49236400-49237400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr3:49236400-49237400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
6	chr3:49236400-49237400	Active TSS	Brain Anterior Caudate	brain
7	chr3:49236400-49237400	Active TSS	Brain Substantia Nigra	brain
8	chr3:49236400-49237400	Active TSS	Colon Smooth Muscle	Colon
9	chr3:49236400-49237400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
10	chr3:49236400-49237400	Bivalent/Poised TSS	Fetal Brain Female	brain
11	chr3:49236400-49237400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
12	chr3:49236400-49237400	Active TSS	Fetal Kidney	kidney
13	chr3:49236400-49237400	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr3:49236400-49237600	Active TSS	Aorta	Aorta
15	chr3:49236400-49237600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr3:49236400-49237600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr3:49236400-49237600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
18	chr3:49236400-49237600	Active TSS	Psoas Muscle	Psoas
19	chr3:49236400-49237600	Active TSS	HUVEC	blood vessel
20	chr3:49236400-49237800	Active TSS	Rectal Smooth Muscle	rectum
21	chr3:49236600-49237400	Active TSS	Brain Cingulate Gyrus	brain
22	chr3:49236600-49237400	Active TSS	Colonic Mucosa	Colon
23	chr3:49236600-49237400	Active TSS	HSMM	muscle
24	chr3:49236600-49237600	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr3:49236600-49237800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:49236600-49237800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:49236600-49237800	Active TSS	Ovary	ovary
28	chr3:49236600-49237800	Active TSS	NHDF-Ad	bronchial
29	chr3:49236600-49238000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:49236600-49238000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:49236600-49238200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:49236600-49238200	Active TSS	NHLF	lung
33	chr3:49236800-49237400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
34	chr3:49236800-49237400	Active TSS	Esophagus	oesophagus
35	chr3:49236800-49237600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
36	chr3:49236800-49237600	Active TSS	Left Ventricle	heart
37	chr3:49236800-49237600	Active TSS	Lung	lung
38	chr3:49236800-49237600	Active TSS	Right Atrium	heart
39	chr3:49236800-49237600	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr3:49236800-49237800	Flanking Active TSS	Fetal Muscle Trunk	muscle
41	chr3:49236800-49237800	Active TSS	Right Ventricle	heart
42	chr3:49236800-49238000	Active TSS	Osteobl	bone
43	chr3:49236800-49240600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:49237000-49237400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:49237000-49237400	Active TSS	Pancreas	Pancrea
46	chr3:49237000-49237400	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr3:49237000-49237600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr3:49237000-49237600	Active TSS	NH-A	brain
49	chr3:49237000-49237800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:49237000-49237800	Active TSS	Stomach Smooth Muscle	stomach

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