Variant report

Variant	rs4594940
Chromosome Location	chr6:25195998-25195999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25175400..25178845-chr6:25193942..25196785,3	MCF-7	breast:
2	chr6:25192599..25195454-chr6:25195592..25197372,2	MCF-7	breast:
3	chr6:25193446..25197455-chr6:25200337..25204634,8	MCF-7	breast:
4	chr6:25193165..25196605-chr6:25196765..25200177,4	MCF-7	breast:
5	chr6:24719199..24721942-chr6:25193498..25196051,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264238	Chromatin interaction
ENSG00000222373	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11965121	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs12203442	1.00[CHB][hapmap]
rs1810471	1.00[CHB][hapmap]
rs2328863	1.00[CEU][hapmap]
rs2328865	1.00[CEU][hapmap]
rs2328868	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2328869	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2690056	1.00[CHB][hapmap]
rs2690062	1.00[CHB][hapmap]
rs2690066	1.00[CHB][hapmap]
rs2744263	1.00[CHB][hapmap]
rs2744273	1.00[CHB][hapmap]
rs2744274	1.00[CHB][hapmap]
rs2744279	1.00[CHB][hapmap]
rs2744281	1.00[CHB][hapmap]
rs2744286	1.00[CHB][hapmap]
rs303005	1.00[CHB][hapmap]
rs4711081	1.00[CEU][hapmap]
rs6456661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6902634	1.00[CEU][hapmap]
rs7743508	1.00[CHB][hapmap]
rs7743997	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv462663	chr6:25156197-25234884	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv601167	chr6:25156197-25234884	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25193600-25196200	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:25193600-25196600	Weak transcription	Aorta	Aorta
3	chr6:25193600-25197200	Weak transcription	Fetal Kidney	kidney
4	chr6:25193600-25202200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:25194800-25197000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:25194800-25198200	Weak transcription	Esophagus	oesophagus
7	chr6:25194800-25199000	Enhancers	Hela-S3	cervix
8	chr6:25195000-25196600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:25195000-25197000	Weak transcription	Stomach Mucosa	stomach
10	chr6:25195000-25198000	Weak transcription	Placenta	Placenta
11	chr6:25195000-25198800	Weak transcription	Ovary	ovary
12	chr6:25195000-25202600	Weak transcription	HUVEC	blood vessel
13	chr6:25195000-25203000	Weak transcription	NH-A	brain
14	chr6:25195200-25196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:25195200-25196400	Weak transcription	Osteobl	bone
16	chr6:25195400-25196400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr6:25195400-25196400	Weak transcription	HSMM	muscle

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