Variant report

Variant	rs6964780
Chromosome Location	chr7:4885221-4885222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:4885093..4886145-chr7:4923054..4923575,3	K562	blood:
2	chr7:4874680..4876574-chr7:4882642..4885395,2	MCF-7	breast:
3	chr7:4879131..4881238-chr7:4883956..4886744,2	K562	blood:

Variant related genes	Relation type
ENSG00000157927	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10225766	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10229247	0.96[ASN][1000 genomes]
rs10232563	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10235539	0.81[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs10235701	0.99[ASN][1000 genomes]
rs10275805	0.90[CHB][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap]
rs11982597	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13227970	0.91[ASN][1000 genomes]
rs13242220	0.89[ASN][1000 genomes]
rs1553960	0.90[CHB][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs3750009	0.90[CHB][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.82[LWK][hapmap];0.82[ASN][1000 genomes]
rs4720427	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap]
rs55709921	0.92[ASN][1000 genomes]
rs56008584	0.96[ASN][1000 genomes]
rs6463120	0.96[ASN][1000 genomes]
rs6463135	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6948173	0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6950905	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs6958275	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958439	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6966725	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6969146	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6970381	0.83[ASN][1000 genomes]
rs6976105	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6976625	0.82[ASN][1000 genomes]
rs7385697	0.83[ASN][1000 genomes]
rs7385698	0.83[ASN][1000 genomes]
rs7776704	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7789495	0.99[ASN][1000 genomes]
rs7799569	0.96[ASN][1000 genomes]
rs7799814	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7803124	0.96[ASN][1000 genomes]
rs7806541	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv887378	chr7:4730535-4929721	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv887380	chr7:4760124-4929721	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv471293	chr7:4764861-4885221	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv823994	chr7:4792385-4928328	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv8033	chr7:4802287-5086597	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv1022678	chr7:4810626-5113387	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv538705	chr7:4810626-5113387	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv528748	chr7:4820581-5010993	Enhancers Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1029123	chr7:4821734-4919277	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1021170	chr7:4831361-5058033	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv538706	chr7:4831361-5058033	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv1025467	chr7:4850447-5021443	ZNF genes & repeats Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv605979	chr7:4854592-4944514	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1021999	chr7:4862082-5003190	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv538707	chr7:4862082-5003190	Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv1033855	chr7:4862677-5069764	Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv605980	chr7:4876057-5003373	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4876200-4890400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:4878200-4885400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:4878200-4885400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:4878400-4885400	Weak transcription	Right Atrium	heart
5	chr7:4878600-4885400	Weak transcription	Right Ventricle	heart
6	chr7:4878800-4885400	Weak transcription	Fetal Brain Male	brain
7	chr7:4882200-4885400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:4882200-4885400	Weak transcription	Pancreas	Pancrea
9	chr7:4882600-4885400	Weak transcription	Fetal Kidney	kidney
10	chr7:4882800-4885400	Weak transcription	Ovary	ovary
11	chr7:4883000-4889000	Weak transcription	Fetal Stomach	stomach
12	chr7:4884800-4885400	Enhancers	Brain Germinal Matrix	brain
13	chr7:4885000-4885400	Enhancers	Fetal Lung	lung
14	chr7:4885000-4885600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:4885000-4885600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr7:4885200-4885400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr7:4885200-4885400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:4885200-4885400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:4885200-4885400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr7:4885200-4885600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr7:4885200-4885600	Active TSS	Brain Cingulate Gyrus	brain
22	chr7:4885200-4885800	Enhancers	Primary B cells from peripheral blood	blood
23	chr7:4885200-4885800	Active TSS	Brain Anterior Caudate	brain
24	chr7:4885200-4885800	Active TSS	K562	blood
25	chr7:4885200-4886000	Active TSS	Brain Hippocampus Middle	brain
26	chr7:4885200-4886000	Active TSS	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links