Variant report

Variant	rs916539
Chromosome Location	chr6:25122715-25122716
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1002539	0.90[YRI][hapmap]
rs1037168	0.90[YRI][hapmap]
rs1046141	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs1046142	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128826	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128827	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963128	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11965266	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332924	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12333217	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12333219	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12333222	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12333327	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447242	0.90[YRI][hapmap]
rs160035	0.87[EUR][1000 genomes]
rs16890032	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890067	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890087	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890100	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394361	0.87[EUR][1000 genomes]
rs2516576	1.00[CEU][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]
rs2516578	0.92[AFR][1000 genomes]
rs302983	0.85[YRI][hapmap]
rs3792978	0.90[YRI][hapmap]
rs3812107	0.90[YRI][hapmap]
rs3828730	0.90[YRI][hapmap]
rs3828731	0.90[YRI][hapmap]
rs4538700	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712884	0.85[YRI][hapmap]
rs6456647	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs6456648	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905460	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905554	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905624	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906421	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6913324	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913346	0.91[AFR][1000 genomes]
rs6915329	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925889	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926671	0.86[AFR][1000 genomes]
rs6928763	0.90[YRI][hapmap]
rs733535	0.85[EUR][1000 genomes]
rs7740848	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745550	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745609	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755584	0.95[YRI][hapmap];0.92[AFR][1000 genomes]
rs7756507	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762804	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773107	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774557	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895674	0.85[EUR][1000 genomes]
rs895675	0.85[EUR][1000 genomes]
rs916537	1.00[CEU][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]
rs916538	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461096	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461098	0.90[YRI][hapmap]
rs9461101	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461104	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461106	0.97[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9467388	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs9467394	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467395	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467396	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467397	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467398	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467399	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467400	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467401	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467403	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467404	0.88[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467405	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467406	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467407	0.86[AFR][1000 genomes]
rs9467408	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467409	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467410	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467411	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs916539	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
2	chr6:25091800-25127800	Weak transcription	Esophagus	oesophagus
3	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
4	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:25108800-25125800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:25110200-25123600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:25110400-25122800	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:25110800-25133400	Weak transcription	Aorta	Aorta
9	chr6:25113000-25136800	Weak transcription	Osteobl	bone
10	chr6:25113400-25124200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr6:25113600-25132800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:25114000-25130600	Weak transcription	Fetal Lung	lung
13	chr6:25114600-25125800	Weak transcription	GM12878-XiMat	blood
14	chr6:25114800-25123000	Weak transcription	Spleen	Spleen
15	chr6:25114800-25123200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:25114800-25123600	Weak transcription	Thymus	Thymus
17	chr6:25114800-25124800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:25114800-25125800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:25114800-25127800	Weak transcription	Left Ventricle	heart
20	chr6:25115000-25122800	Weak transcription	Liver	Liver
21	chr6:25115800-25123600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:25115800-25124000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:25116000-25123000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:25116000-25123600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:25116000-25137000	Weak transcription	Lung	lung
26	chr6:25119000-25123800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:25119000-25124000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:25119800-25123000	Weak transcription	Primary T cells from cord blood	blood
29	chr6:25120000-25123000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:25120000-25123800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:25120000-25123800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:25120000-25124400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:25120000-25124600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:25120000-25127800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr6:25120600-25123600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr6:25120600-25124800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:25120600-25129800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:25120800-25124800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:25120800-25127800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:25121000-25129800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:25121200-25124600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr6:25121200-25125000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr6:25121200-25127800	Strong transcription	Dnd41	blood
44	chr6:25121400-25123200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:25121600-25122800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:25121600-25124600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:25121600-25127200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:25121800-25122800	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr6:25121800-25122800	Enhancers	HUVEC	blood vessel
50	chr6:25121800-25123200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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