Variant report

Variant	rs4954914
Chromosome Location	chr2:142266867-142266868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:142265321..142267918-chr2:142664161..142666622,2	MCF-7	breast:
2	chr2:142261934..142264280-chr2:142265309..142267485,3	MCF-7	breast:
3	chr2:142259654..142261746-chr2:142265611..142267711,3	MCF-7	breast:
4	chr2:142263240..142267352-chr2:142886657..142889435,3	MCF-7	breast:
5	chr2:142223533..142226548-chr2:142266133..142269163,3	MCF-7	breast:
6	chr2:142241833..142244486-chr2:142265674..142268047,2	MCF-7	breast:
7	chr2:142265220..142267079-chr2:142275773..142278354,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168702	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10496881	0.85[JPT][hapmap]
rs11887304	0.86[JPT][hapmap]
rs13419140	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1483144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16846216	0.86[JPT][hapmap]
rs16846224	0.85[JPT][hapmap]
rs16846251	0.86[JPT][hapmap]
rs16846274	0.85[JPT][hapmap]
rs16846416	0.85[JPT][hapmap]
rs16846509	0.85[JPT][hapmap]
rs16846539	0.86[JPT][hapmap]
rs16855055	0.86[JPT][hapmap]
rs1905291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34962994	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41396347	0.85[JPT][hapmap]
rs4408668	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4491668	0.86[JPT][hapmap]
rs4547471	0.86[JPT][hapmap]
rs4560051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4575660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4954915	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55869530	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6429898	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6749551	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9287319	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875240	chr2:142199421-142347455	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv470491	chr2:142254119-142299923	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv834393	chr2:142256714-142431564	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
6	nsv583210	chr2:142259592-142295042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv459629	chr2:142263400-142295042	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv583211	chr2:142263400-142295042	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv583212	chr2:142263979-142309330	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142264000-142268000	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:142266000-142267200	Enhancers	A549	lung
3	chr2:142266200-142267600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:142266200-142267600	Enhancers	Brain Anterior Caudate	brain
5	chr2:142266400-142267200	Enhancers	Brain Cingulate Gyrus	brain
6	chr2:142266600-142267000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:142266600-142268800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:142266800-142267000	Enhancers	Brain Substantia Nigra	brain

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