Variant report

Variant	rs6439642
Chromosome Location	chr3:136192807-136192808
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr3:136192566-136193043	IMR90	lung:	n/a	chr3:136192719-136192735 chr3:136192723-136192733 chr3:136192717-136192737 chr3:136192721-136192730 chr3:136192720-136192734 chr3:136192724-136192733

Variant related genes	Relation type
STAG1	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10513002	1.00[CHB][hapmap]
rs10513016	1.00[CHB][hapmap]
rs12330800	0.85[EUR][1000 genomes]
rs12635723	0.88[YRI][hapmap]
rs1279425	0.86[YRI][hapmap]
rs13433980	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs1484250	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs16843879	1.00[CHB][hapmap]
rs16843978	1.00[CHB][hapmap]
rs16843991	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17199978	1.00[CHB][hapmap]
rs17266364	1.00[CHB][hapmap]
rs17365351	1.00[CHB][hapmap]
rs28396702	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34165586	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34962604	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35644083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3931416	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs3932048	0.95[CEU][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4678438	0.88[YRI][hapmap]
rs5026242	0.84[EUR][1000 genomes]
rs55993001	0.82[AMR][1000 genomes]
rs56040643	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56125228	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56251259	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59931907	0.85[AMR][1000 genomes]
rs6439638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs66810260	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6765239	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs6766450	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6769934	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773495	1.00[CHB][hapmap]
rs6773604	1.00[CHB][hapmap]
rs6776841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap]
rs6782151	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs6783337	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap]
rs6789541	0.81[AMR][1000 genomes]
rs6789761	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6799368	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800969	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs6804194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6806795	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs699165	0.81[YRI][hapmap]
rs7612160	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7615706	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7620314	0.81[CEU][hapmap]
rs7621017	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7621970	0.85[AMR][1000 genomes]
rs7627292	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7629905	0.83[AFR][1000 genomes]
rs7644346	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs7644471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646563	1.00[CHB][hapmap]
rs7646723	1.00[CHB][hapmap]
rs7648591	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7650075	1.00[CHB][hapmap]
rs923001	1.00[CHB][hapmap]
rs9809184	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9811261	0.82[EUR][1000 genomes]
rs9812319	1.00[CEU][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9812513	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs9819496	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9820513	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9828068	0.83[AFR][1000 genomes]
rs9831321	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9832572	0.85[AMR][1000 genomes]
rs9833162	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap]
rs9834631	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9839574	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs9843801	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs9845762	0.88[YRI][hapmap]
rs9845950	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs9850383	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9853387	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs9854084	0.83[YRI][hapmap]
rs9858457	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860801	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs9866535	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868120	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136194200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:136176400-136194400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:136176400-136194400	Weak transcription	HSMM	muscle
4	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:136176600-136195000	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:136176600-136195000	Weak transcription	Spleen	Spleen
7	chr3:136176600-136196600	Weak transcription	HUVEC	blood vessel
8	chr3:136176600-136212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:136176600-136222800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:136176600-136224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:136176600-136224400	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:136176600-136231800	Weak transcription	Psoas Muscle	Psoas
13	chr3:136176600-136240000	Weak transcription	HMEC	breast
14	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:136176800-136193400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:136176800-136193400	Weak transcription	Esophagus	oesophagus
17	chr3:136176800-136193600	Weak transcription	Ovary	ovary
18	chr3:136176800-136194400	Weak transcription	Brain Anterior Caudate	brain
19	chr3:136176800-136194400	Weak transcription	Brain Germinal Matrix	brain
20	chr3:136176800-136194800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:136176800-136205800	Weak transcription	Small Intestine	intestine
22	chr3:136176800-136228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
24	chr3:136177200-136236400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:136177400-136198400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:136177600-136193400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:136178000-136194600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:136178000-136212000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:136178400-136193400	Weak transcription	Fetal Brain Female	brain
30	chr3:136178400-136208200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:136178600-136194400	Weak transcription	Brain Angular Gyrus	brain
32	chr3:136178600-136220200	Weak transcription	Fetal Brain Male	brain
33	chr3:136179400-136204000	Weak transcription	Fetal Intestine Small	intestine
34	chr3:136179800-136212000	Weak transcription	Fetal Heart	heart
35	chr3:136181200-136205400	Weak transcription	Fetal Kidney	kidney
36	chr3:136181400-136211600	Weak transcription	A549	lung
37	chr3:136181800-136196000	Weak transcription	K562	blood
38	chr3:136182000-136204400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:136182200-136193200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:136183600-136195000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:136183800-136193400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:136183800-136195000	Weak transcription	Aorta	Aorta
43	chr3:136183800-136212000	Weak transcription	Lung	lung
44	chr3:136184400-136194200	Weak transcription	Thymus	Thymus
45	chr3:136184400-136194600	Weak transcription	Right Ventricle	heart
46	chr3:136185200-136194800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:136186000-136194400	Weak transcription	HSMMtube	muscle
48	chr3:136189400-136196600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:136189800-136193200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:136189800-136195600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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