Variant report

Variant	rs12631306
Chromosome Location	chr3:50003305-50003306
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11130223	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130225	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130239	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130240	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11920034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11923132	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11924711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11925156	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11928995	0.84[AMR][1000 genomes]
rs12486470	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12486808	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486832	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492291	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12493565	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494077	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494172	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494916	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12495114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12495831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629677	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630917	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12630959	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12631248	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12631309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631608	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632751	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12636232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs12636669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637222	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637681	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12638046	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1317215	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs13326300	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2023951	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2023952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2188151	1.00[JPT][hapmap]
rs28478136	0.92[EUR][1000 genomes]
rs41291716	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55643042	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57009357	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57575459	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58025924	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58621288	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58766761	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59802870	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61263937	0.89[EUR][1000 genomes]
rs61491513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61729114	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62260717	0.80[EUR][1000 genomes]
rs62260756	0.92[EUR][1000 genomes]
rs62260770	0.89[AMR][1000 genomes]
rs62260771	0.89[AMR][1000 genomes]
rs62262060	0.92[EUR][1000 genomes]
rs62262095	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262096	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262099	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262100	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262104	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262105	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262116	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262117	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262136	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262138	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262144	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262145	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262148	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263578	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263580	0.88[EUR][1000 genomes]
rs62263584	0.88[EUR][1000 genomes]
rs62263586	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263588	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263590	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263591	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263596	0.89[AMR][1000 genomes]
rs62263597	0.83[AMR][1000 genomes]
rs6797500	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs9813644	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9859813	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978800-50004800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:49978800-50009600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:49978800-50009600	Weak transcription	Fetal Kidney	kidney
4	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:49979000-50003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:49979000-50003600	Weak transcription	Right Ventricle	heart
7	chr3:49979000-50005200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:49979000-50010200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:49979600-50004200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:49980400-50003600	Weak transcription	Brain Angular Gyrus	brain
11	chr3:49983800-50003400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:49988000-50003600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:49988000-50004200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:49988200-50007000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:49988200-50007400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:49988200-50010200	Weak transcription	Gastric	stomach
17	chr3:49988200-50010600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:49988400-50009600	Weak transcription	Fetal Brain Female	brain
19	chr3:49988400-50009600	Weak transcription	HUVEC	blood vessel
20	chr3:49988800-50004800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:49989000-50004000	Weak transcription	Pancreas	Pancrea
22	chr3:49991200-50005800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:49992200-50037000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:49995000-50005200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:49995400-50033200	Weak transcription	Fetal Brain Male	brain
26	chr3:49995600-50005800	Weak transcription	Spleen	Spleen
27	chr3:49996400-50003600	Weak transcription	HMEC	breast
28	chr3:49996600-50010200	Weak transcription	Lung	lung
29	chr3:49997000-50010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:49997600-50007400	Weak transcription	Right Atrium	heart
31	chr3:49997600-50009600	Weak transcription	A549	lung
32	chr3:49997800-50003600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:49997800-50003600	Weak transcription	Brain Substantia Nigra	brain
34	chr3:49997800-50004000	Weak transcription	Brain Anterior Caudate	brain
35	chr3:49997800-50004000	Weak transcription	Left Ventricle	heart
36	chr3:49997800-50009600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:49997800-50009800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:49997800-50013800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:49998200-50003800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:49998200-50003800	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:49998200-50007600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:49998400-50003600	Weak transcription	Fetal Lung	lung
44	chr3:49998400-50003800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:49998400-50003800	Weak transcription	NHLF	lung
46	chr3:49998400-50004000	Weak transcription	NHDF-Ad	bronchial
47	chr3:49998400-50004800	Weak transcription	Thymus	Thymus
48	chr3:49998400-50029600	Weak transcription	Fetal Heart	heart
49	chr3:49998400-50078600	Weak transcription	K562	blood
50	chr3:49998800-50003800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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