Variant report

Variant	rs3828731
Chromosome Location	chr6:25087555-25087556
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1002539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1002540	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037167	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046141	0.95[YRI][hapmap]
rs1046142	0.95[YRI][hapmap]
rs11757374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12332924	0.95[YRI][hapmap]
rs12333217	0.95[YRI][hapmap]
rs13209444	0.86[ASN][1000 genomes]
rs1447242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890067	0.95[YRI][hapmap]
rs16890087	0.95[YRI][hapmap]
rs16890100	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs2273671	0.83[ASN][1000 genomes]
rs2516576	0.90[YRI][hapmap]
rs302983	0.95[YRI][hapmap]
rs36078207	0.83[ASN][1000 genomes]
rs3792974	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs3792976	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792982	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792983	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs3812107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4538700	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs4711074	0.94[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];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712884	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456647	0.95[YRI][hapmap]
rs6456648	0.95[YRI][hapmap]
rs6905460	0.95[YRI][hapmap]
rs6905554	0.90[YRI][hapmap]
rs6905624	0.95[YRI][hapmap]
rs6913324	0.95[YRI][hapmap]
rs6915329	0.95[YRI][hapmap]
rs6925889	0.95[YRI][hapmap]
rs6928752	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6928763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555176	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72826363	0.87[ASN][1000 genomes]
rs7738141	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs7740848	0.95[YRI][hapmap]
rs7745550	0.95[YRI][hapmap]
rs7745609	0.95[YRI][hapmap]
rs7755584	0.95[YRI][hapmap]
rs7762804	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs7773107	0.95[YRI][hapmap]
rs7774557	0.95[YRI][hapmap]
rs916537	0.90[YRI][hapmap]
rs916538	0.90[YRI][hapmap]
rs916539	0.90[YRI][hapmap]
rs9461096	0.81[YRI][hapmap]
rs9461098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461104	0.90[YRI][hapmap]
rs9467386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467388	0.95[YRI][hapmap]
rs9467392	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9467395	0.95[YRI][hapmap]
rs9467396	0.95[YRI][hapmap]
rs9467400	0.95[YRI][hapmap]
rs9467401	0.95[YRI][hapmap]
rs9467404	0.95[YRI][hapmap]
rs9467405	0.95[YRI][hapmap]
rs9467409	0.95[YRI][hapmap]
rs9467410	0.95[YRI][hapmap]
rs9467411	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25079400-25093000	Weak transcription	Ovary	ovary
2	chr6:25080400-25098000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:25081200-25092000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:25081600-25088800	Weak transcription	Osteobl	bone
5	chr6:25082200-25094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:25083800-25089800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:25083800-25093200	Weak transcription	Colonic Mucosa	Colon
9	chr6:25084000-25087600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:25084200-25089800	Weak transcription	Hela-S3	cervix
11	chr6:25084800-25088400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr6:25084800-25099000	Weak transcription	Fetal Intestine Large	intestine
13	chr6:25084800-25113800	Weak transcription	Gastric	stomach
14	chr6:25085000-25088600	Weak transcription	Lung	lung
15	chr6:25085000-25088600	Enhancers	HUVEC	blood vessel
16	chr6:25085200-25087600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:25085200-25087600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:25085200-25088000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr6:25085200-25089400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr6:25085200-25108000	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:25085400-25088200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:25085400-25091600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:25085600-25087800	Enhancers	Primary B cells from peripheral blood	blood
24	chr6:25085600-25088000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr6:25085800-25088400	Genic enhancers	Dnd41	blood
26	chr6:25086200-25087800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:25086200-25088600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:25086200-25096400	Strong transcription	Thymus	Thymus
29	chr6:25086400-25089800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:25086400-25099600	Strong transcription	Placenta	Placenta
31	chr6:25086600-25090000	Strong transcription	Stomach Smooth Muscle	stomach
32	chr6:25086600-25090400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:25086600-25096600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr6:25086800-25087600	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr6:25086800-25087600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr6:25086800-25087600	Strong transcription	Small Intestine	intestine
37	chr6:25086800-25087800	Strong transcription	HSMMtube	muscle
38	chr6:25086800-25088200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:25086800-25088800	Enhancers	Primary T cells from cord blood	blood
40	chr6:25086800-25088800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:25087000-25087800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr6:25087000-25089000	Weak transcription	Liver	Liver
43	chr6:25087000-25090600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr6:25087000-25093000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:25087000-25105400	Weak transcription	GM12878-XiMat	blood
46	chr6:25087200-25089000	Weak transcription	Spleen	Spleen
47	chr6:25087200-25090200	Genic enhancers	Primary hematopoietic stem cells	blood
48	chr6:25087200-25091400	Weak transcription	Esophagus	oesophagus
49	chr6:25087400-25087800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr6:25087400-25088400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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