Variant report

Variant	rs3812109
Chromosome Location	chr6:25082678-25082679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1002539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1002540	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037167	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13209444	0.86[ASN][1000 genomes]
rs1447242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192773	0.85[CEU][hapmap]
rs2273671	0.85[CEU][hapmap];0.83[ASN][1000 genomes]
rs303879	0.85[CEU][hapmap]
rs303880	0.85[CEU][hapmap]
rs36078207	0.83[ASN][1000 genomes]
rs3792974	0.81[CEU][hapmap];0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs3792976	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792977	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792982	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792983	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs3812107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs3828730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711074	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711075	0.86[ASN][1000 genomes]
rs4711076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712884	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928752	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6928763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555176	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72826363	0.87[ASN][1000 genomes]
rs7738141	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs9461098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467392	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking 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	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25067600-25084600	Weak transcription	HSMMtube	muscle
2	chr6:25069800-25084000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:25071000-25084400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:25071200-25083800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:25071200-25083800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:25071200-25084000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:25071200-25084000	Weak transcription	Placenta	Placenta
8	chr6:25071200-25084000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:25071200-25084600	Weak transcription	Adipose Nuclei	Adipose
10	chr6:25071200-25085200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:25071200-25085400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:25071400-25084800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:25071400-25085600	Weak transcription	Primary B cells from cord blood	blood
14	chr6:25076200-25084200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:25077000-25086600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:25079200-25083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:25079400-25085200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:25079400-25093000	Weak transcription	Ovary	ovary
19	chr6:25079600-25086800	Weak transcription	Aorta	Aorta
20	chr6:25079800-25086800	Weak transcription	Spleen	Spleen
21	chr6:25080000-25082800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:25080200-25085800	Strong transcription	Dnd41	blood
23	chr6:25080400-25084000	Weak transcription	Gastric	stomach
24	chr6:25080400-25085200	Strong transcription	Thymus	Thymus
25	chr6:25080400-25085400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:25080400-25098000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:25080600-25084600	Strong transcription	Primary hematopoietic stem cells	blood
28	chr6:25080600-25084800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:25080800-25084200	Weak transcription	Lung	lung
30	chr6:25080800-25085000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:25080800-25085400	Strong transcription	Fetal Thymus	thymus
32	chr6:25081000-25086600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:25081200-25083800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:25081200-25084000	Weak transcription	Left Ventricle	heart
35	chr6:25081200-25084800	Weak transcription	Primary T cells from cord blood	blood
36	chr6:25081200-25092000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:25081600-25084600	Weak transcription	Fetal Heart	heart
38	chr6:25081600-25088800	Weak transcription	Osteobl	bone
39	chr6:25082000-25085000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr6:25082200-25083000	Enhancers	Liver	Liver
41	chr6:25082200-25083800	Enhancers	HepG2	liver
42	chr6:25082200-25094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:25082400-25083000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr6:25082400-25083200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:25082400-25085200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:25082400-25085600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr6:25082600-25083000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:25082600-25084800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr6:25082600-25085200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum

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