Variant report

Variant	rs12625704
Chromosome Location	chr20:13694028-13694029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10485767	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap]
rs11696168	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12625600	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789336	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs4813143	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]
rs4814253	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6105151	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105160	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6105163	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs6110019	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110023	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6110037	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap]
rs6110050	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6514441	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7360405	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs736365	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	esv1793063	chr20:13691562-13708788	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13689000-13694400	Weak transcription	Primary B cells from cord blood	blood
2	chr20:13690200-13696400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr20:13690400-13697000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr20:13690600-13695600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr20:13690600-13706200	Weak transcription	Pancreas	Pancrea
6	chr20:13691200-13695400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:13691400-13694200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr20:13691400-13694200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr20:13691400-13694200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr20:13691400-13694200	Weak transcription	Osteobl	bone
11	chr20:13691400-13696000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr20:13691400-13696200	Weak transcription	Right Ventricle	heart
13	chr20:13691600-13694400	Weak transcription	HSMM	muscle
14	chr20:13691600-13694600	Weak transcription	NH-A	brain
15	chr20:13691600-13695000	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr20:13691600-13696000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr20:13691800-13694200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr20:13691800-13695400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr20:13691800-13699000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr20:13691800-13706200	Weak transcription	Aorta	Aorta
21	chr20:13691800-13708000	Weak transcription	Fetal Brain Male	brain
22	chr20:13692000-13694400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr20:13692000-13696000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr20:13692200-13694200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr20:13692200-13694200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr20:13692200-13694200	Weak transcription	HepG2	liver
27	chr20:13692200-13694400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr20:13692200-13694400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr20:13692200-13694400	Weak transcription	Brain Hippocampus Middle	brain
30	chr20:13692200-13695200	Weak transcription	Fetal Lung	lung
31	chr20:13692200-13695600	Weak transcription	Thymus	Thymus
32	chr20:13692200-13696000	Weak transcription	Brain Angular Gyrus	brain
33	chr20:13692200-13696000	Weak transcription	Lung	lung
34	chr20:13692200-13696000	Weak transcription	Ovary	ovary
35	chr20:13692200-13696000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr20:13692200-13696200	Weak transcription	Brain Anterior Caudate	brain
37	chr20:13692200-13696800	Weak transcription	Spleen	Spleen
38	chr20:13692200-13698800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr20:13692200-13699800	Strong transcription	A549	lung
40	chr20:13692200-13709200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr20:13692200-13712200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr20:13692200-13712400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr20:13692200-13745000	Weak transcription	Small Intestine	intestine
44	chr20:13692400-13694400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr20:13692400-13694600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr20:13692400-13695400	Weak transcription	Brain Substantia Nigra	brain
47	chr20:13692400-13696000	Weak transcription	Fetal Brain Female	brain
48	chr20:13692400-13696000	Weak transcription	HSMMtube	muscle
49	chr20:13692400-13698600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr20:13692400-13712400	Weak transcription	Brain Germinal Matrix	brain

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