Variant report

Variant	rs1046141
Chromosome Location	chr6:25113854-25113855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25111673..25113955-chr6:25164740..25166276,2	MCF-7	breast:
2	chr6:25110856..25114923-chr6:25121965..25124614,3	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1002539	0.95[YRI][hapmap]
rs1037168	0.94[YRI][hapmap]
rs1046142	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1128826	0.88[AFR][1000 genomes]
rs1128827	0.87[AFR][1000 genomes]
rs12332924	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12333217	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12333219	0.87[AFR][1000 genomes]
rs12333222	0.87[AFR][1000 genomes]
rs12333327	0.88[AFR][1000 genomes]
rs1447242	0.95[YRI][hapmap]
rs16890067	0.86[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs16890087	0.86[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs16890100	1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1880271	1.00[CHD][hapmap]
rs1900552	1.00[CHD][hapmap]
rs2044553	1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2516576	0.95[LWK][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs2516578	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2690047	1.00[CHD][hapmap]
rs2690076	1.00[CHD][hapmap]
rs2690102	1.00[CHD][hapmap]
rs2690124	1.00[CHD][hapmap]
rs2744282	1.00[CHD][hapmap]
rs302983	0.90[YRI][hapmap]
rs3792978	0.95[YRI][hapmap]
rs3812107	0.95[YRI][hapmap]
rs3828730	0.95[YRI][hapmap]
rs3828731	0.95[YRI][hapmap]
rs4538700	0.95[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4711076	0.83[YRI][hapmap]
rs4712884	0.89[YRI][hapmap]
rs6456647	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6456648	1.00[YRI][hapmap]
rs6456653	1.00[CHD][hapmap]
rs6905460	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6905554	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs6905624	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6906421	0.91[AFR][1000 genomes]
rs6913324	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6913346	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6915329	0.82[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6925889	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6926671	0.92[AFR][1000 genomes]
rs6928763	0.95[YRI][hapmap]
rs7739830	1.00[CHD][hapmap]
rs7740848	0.86[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7745550	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7745609	0.88[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7755584	1.00[ASW][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7756507	0.87[AFR][1000 genomes]
rs7762804	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7773107	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7774557	0.86[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs916537	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs916538	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs916539	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs940405	1.00[CHD][hapmap]
rs9461096	0.89[YRI][hapmap]
rs9461098	0.95[YRI][hapmap]
rs9461101	0.87[AFR][1000 genomes]
rs9461104	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs9461106	0.88[AFR][1000 genomes]
rs9467388	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9467394	0.87[AFR][1000 genomes]
rs9467395	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9467396	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9467398	0.87[AFR][1000 genomes]
rs9467400	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9467401	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9467403	0.88[AFR][1000 genomes]
rs9467404	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9467405	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9467406	0.88[AFR][1000 genomes]
rs9467407	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9467408	0.88[AFR][1000 genomes]
rs9467409	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9467410	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9467411	0.95[YRI][hapmap];0.91[AFR][1000 genomes]

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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
2	chr6:25091600-25116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:25091800-25127800	Weak transcription	Esophagus	oesophagus
4	chr6:25096000-25116000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:25096400-25118200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:25099000-25116200	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:25099000-25117400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:25101400-25115800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:25102000-25116200	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr6:25102800-25117600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:25103200-25116000	Strong transcription	Primary hematopoietic stem cells	blood
12	chr6:25103200-25116000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr6:25103400-25116000	Strong transcription	Primary T cells from cord blood	blood
14	chr6:25103600-25116000	Strong transcription	HSMMtube	muscle
15	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
16	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:25105200-25116000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:25105600-25115600	Weak transcription	Pancreas	Pancrea
19	chr6:25105600-25116000	Strong transcription	Placenta	Placenta
20	chr6:25105800-25115000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:25105800-25115000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:25106000-25115600	Weak transcription	Right Ventricle	heart
23	chr6:25106000-25119800	Weak transcription	Fetal Intestine Small	intestine
24	chr6:25106400-25122200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:25107200-25122200	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:25108600-25116000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr6:25108800-25116400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:25108800-25122000	Weak transcription	Colonic Mucosa	Colon
29	chr6:25108800-25125800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:25109600-25114600	Strong transcription	GM12878-XiMat	blood
31	chr6:25110200-25123600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:25110400-25122800	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:25110800-25114200	Weak transcription	Ovary	ovary
34	chr6:25110800-25133400	Weak transcription	Aorta	Aorta
35	chr6:25111000-25114600	Enhancers	Hela-S3	cervix
36	chr6:25111000-25116000	Strong transcription	Primary B cells from cord blood	blood
37	chr6:25111600-25114800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:25112400-25114800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:25112400-25114800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
40	chr6:25112400-25114800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:25112400-25114800	Strong transcription	Thymus	Thymus
42	chr6:25112400-25115800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:25112600-25115800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:25112800-25114600	Genic enhancers	Liver	Liver
45	chr6:25112800-25114800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr6:25112800-25116000	Strong transcription	Lung	lung
47	chr6:25112800-25116600	Weak transcription	Fetal Stomach	stomach
48	chr6:25113000-25114800	Strong transcription	Adipose Nuclei	Adipose
49	chr6:25113000-25115000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:25113000-25136800	Weak transcription	Osteobl	bone

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