Variant report

Variant	rs6946425
Chromosome Location	chr7:7551108-7551109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7547719..7549678-chr7:7550952..7552917,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1013002	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes]
rs1016028	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10952059	1.00[MEX][hapmap]
rs11773679	1.00[CEU][hapmap]
rs11976831	0.95[EUR][1000 genomes]
rs11983756	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12535954	0.82[EUR][1000 genomes]
rs1294600	1.00[AMR][1000 genomes]
rs2051910	0.81[EUR][1000 genomes]
rs2051912	0.81[EUR][1000 genomes]
rs2051913	0.81[EUR][1000 genomes]
rs2051914	0.81[EUR][1000 genomes]
rs2108064	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs2108067	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2190248	0.95[EUR][1000 genomes]
rs2348265	0.81[EUR][1000 genomes]
rs2348339	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2881888	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs3757532	1.00[CEU][hapmap]
rs4035104	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4380838	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4720741	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes]
rs4725005	1.00[CEU][hapmap]
rs6463696	0.82[CEU][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes]
rs6463702	1.00[CEU][hapmap]
rs6463705	0.81[EUR][1000 genomes]
rs6946022	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6948157	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6948448	0.87[EUR][1000 genomes]
rs6957976	1.00[CEU][hapmap]
rs6958110	1.00[CEU][hapmap]
rs6962939	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs6964397	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6974246	0.81[EUR][1000 genomes]
rs7783239	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs7789187	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7789287	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7791344	0.90[EUR][1000 genomes]
rs7791808	0.82[CEU][hapmap]
rs7796709	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7805565	1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs7806046	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7808788	0.95[EUR][1000 genomes]
rs7810367	0.82[EUR][1000 genomes]
rs9640043	0.95[EUR][1000 genomes]
rs9640044	0.81[EUR][1000 genomes]
rs9640045	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs972600	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs974320	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
7	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking 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 miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	nsv606043	chr7:7473563-7571420	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887473	chr7:7497676-7604913	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1027872	chr7:7516124-7600842	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1024107	chr7:7516124-7601638	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
17	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
18	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7528600-7575400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:7529000-7557600	Weak transcription	Pancreas	Pancrea
3	chr7:7542000-7552200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:7545000-7551600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:7545200-7551600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:7545800-7553000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:7546000-7552400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:7546200-7555600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:7546200-7556000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:7546600-7552400	Weak transcription	Stomach Mucosa	stomach
11	chr7:7550400-7551200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:7550400-7551400	Enhancers	NHDF-Ad	bronchial
13	chr7:7550600-7551800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:7551000-7552800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr7:7551000-7556400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links