Variant report

Variant	rs12494916
Chromosome Location	chr3:50119739-50119740
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs11130223	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11130225	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11130230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11130237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11130239	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11130240	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11916261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11916999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923132	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11924670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925156	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11928995	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486470	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486808	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12486832	0.88[EUR][1000 genomes]
rs12489386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12490944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12492291	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493565	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12494077	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494172	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12629129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12629553	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs12629677	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12630917	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12630959	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12631248	1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12631309	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12631608	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12632751	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636045	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636669	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12637222	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12637457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12637681	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12638046	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13100903	0.94[ASN][1000 genomes]
rs1317215	0.84[EUR][1000 genomes]
rs13326300	0.84[EUR][1000 genomes]
rs2003485	0.87[ASN][1000 genomes]
rs2023951	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478136	0.84[EUR][1000 genomes]
rs35333166	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41291716	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55643042	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57009357	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57575459	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58025924	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58621288	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58766761	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59802870	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61491513	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61729114	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62260756	0.84[EUR][1000 genomes]
rs62260770	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260771	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262060	0.84[EUR][1000 genomes]
rs62262095	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62262096	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62262099	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62262100	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62262104	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62262105	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62262116	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62262117	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62262138	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62262144	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62262145	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62262148	0.88[EUR][1000 genomes]
rs62263578	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62263580	0.96[EUR][1000 genomes]
rs62263584	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263586	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263588	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263590	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263591	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263596	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263597	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62263600	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797500	0.84[EUR][1000 genomes]
rs9813644	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9859813	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv822079	chr3:50116177-50126157	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50104200-50123400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:50106200-50125800	Weak transcription	Stomach Mucosa	stomach
3	chr3:50108800-50126000	Weak transcription	Fetal Heart	heart
4	chr3:50110200-50126000	Weak transcription	NHLF	lung
5	chr3:50110600-50125800	Weak transcription	Small Intestine	intestine
6	chr3:50111000-50125800	Weak transcription	Colonic Mucosa	Colon
7	chr3:50111000-50126000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:50111200-50119800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:50111200-50126200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:50112200-50125800	Weak transcription	K562	blood
11	chr3:50113000-50125800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:50113000-50125800	Weak transcription	A549	lung
13	chr3:50113000-50126000	Weak transcription	NH-A	brain
14	chr3:50113200-50120200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:50113200-50120200	Weak transcription	Spleen	Spleen
16	chr3:50113200-50125600	Weak transcription	HepG2	liver
17	chr3:50113200-50125800	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:50113200-50125800	Weak transcription	Gastric	stomach
19	chr3:50113200-50125800	Weak transcription	Pancreas	Pancrea
20	chr3:50113200-50125800	Weak transcription	Psoas Muscle	Psoas
21	chr3:50113200-50126200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:50113400-50125600	Weak transcription	Dnd41	blood
23	chr3:50113400-50125800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:50113400-50125800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:50113400-50125800	Weak transcription	Brain Substantia Nigra	brain
26	chr3:50113400-50125800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:50113400-50125800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:50113400-50125800	Weak transcription	Hela-S3	cervix
29	chr3:50113400-50125800	Weak transcription	HMEC	breast
30	chr3:50113400-50125800	Weak transcription	NHEK	skin
31	chr3:50113400-50126000	Weak transcription	Fetal Kidney	kidney
32	chr3:50113400-50126000	Weak transcription	Fetal Lung	lung
33	chr3:50113400-50126000	Weak transcription	HSMMtube	muscle
34	chr3:50114600-50119800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:50114600-50126000	Weak transcription	Ovary	ovary
36	chr3:50114800-50125800	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:50115400-50125800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:50115400-50125800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:50115400-50125800	Weak transcription	Brain Anterior Caudate	brain
40	chr3:50115400-50125800	Weak transcription	Right Ventricle	heart
41	chr3:50115400-50125800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:50115400-50126000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:50115600-50125800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:50115600-50125800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:50115600-50126000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:50115600-50126000	Weak transcription	Fetal Stomach	stomach
47	chr3:50115600-50126000	Weak transcription	NHDF-Ad	bronchial
48	chr3:50115600-50126400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:50115800-50119800	Weak transcription	Primary T cells from cord blood	blood
50	chr3:50115800-50119800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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