Variant report

Variant	rs3792978
Chromosome Location	chr6:25089660-25089661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:25089592-25090266	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr6:25089602-25090029	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr6:25089626-25089993	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr6:25089652-25090073	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr6:25089657-25090055	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr6:25089587-25090058	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr6:25089652-25090013	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25085087..25087243-chr6:25089273..25091853,2	K562	blood:
2	chr6:25084985..25086769-chr6:25088550..25090244,2	MCF-7	breast:

Variant related genes	Relation type
CMAHP	TF binding region
ENSG00000168405	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1002540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037167	1.00[AFR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];1.00[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];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12332924	0.94[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890067	0.89[ASW][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap]
rs16890087	0.89[ASW][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap]
rs16890100	0.89[ASW][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs2273671	0.89[CHD][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs2516576	0.89[ASW][hapmap];0.83[MKK][hapmap];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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792977	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792983	0.85[CHB][hapmap];0.92[CHD][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs3812107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs3812108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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]
rs3828731	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	0.89[ASW][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs4711074	0.98[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];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712884	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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	0.89[ASW][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap]
rs6925889	0.95[YRI][hapmap]
rs6928752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6928763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs71555176	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72826363	0.87[ASN][1000 genomes]
rs7738141	0.85[CHB][hapmap];0.92[CHD][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs7740848	0.89[ASW][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap]
rs7745550	0.95[YRI][hapmap]
rs7745609	0.89[ASW][hapmap];0.83[MKK][hapmap];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	0.89[ASW][hapmap];0.95[YRI][hapmap]
rs916537	0.90[YRI][hapmap]
rs916538	0.90[YRI][hapmap]
rs916539	0.90[YRI][hapmap]
rs9461096	0.84[YRI][hapmap]
rs9461098	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]
rs9461104	0.90[YRI][hapmap]
rs9467386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467388	0.94[YRI][hapmap]
rs9467392	0.89[AFR][1000 genomes];0.94[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3792978	HIST1H1E	cis	parietal	SCAN

Chromatin state (count:66 , 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	chr6:25082200-25094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:25083800-25089800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:25083800-25093200	Weak transcription	Colonic Mucosa	Colon
8	chr6:25084200-25089800	Weak transcription	Hela-S3	cervix
9	chr6:25084800-25099000	Weak transcription	Fetal Intestine Large	intestine
10	chr6:25084800-25113800	Weak transcription	Gastric	stomach
11	chr6:25085200-25108000	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:25085400-25091600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:25086200-25096400	Strong transcription	Thymus	Thymus
14	chr6:25086400-25089800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:25086400-25099600	Strong transcription	Placenta	Placenta
16	chr6:25086600-25090000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr6:25086600-25090400	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:25086600-25096600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr6:25087000-25090600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:25087000-25093000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:25087000-25105400	Weak transcription	GM12878-XiMat	blood
22	chr6:25087200-25090200	Genic enhancers	Primary hematopoietic stem cells	blood
23	chr6:25087200-25091400	Weak transcription	Esophagus	oesophagus
24	chr6:25087400-25089800	Weak transcription	Left Ventricle	heart
25	chr6:25087400-25092200	Weak transcription	Primary B cells from cord blood	blood
26	chr6:25087400-25098200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:25087400-25101600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:25087400-25113800	Strong transcription	Fetal Thymus	thymus
29	chr6:25087600-25091200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:25087600-25105400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
32	chr6:25087800-25093000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:25087800-25093400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:25087800-25097200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:25088000-25105800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:25088200-25091200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:25088400-25090200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:25088400-25090400	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr6:25088400-25096600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:25088400-25105400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr6:25088400-25113800	Strong transcription	Dnd41	blood
42	chr6:25088600-25089800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:25088600-25090000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:25088600-25090000	Enhancers	NH-A	brain
45	chr6:25088600-25090400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:25088600-25090400	Enhancers	HMEC	breast
47	chr6:25088600-25090400	Enhancers	NHEK	skin
48	chr6:25088600-25090600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr6:25088600-25090800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:25088600-25098000	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links