Variant report

Variant	rs4954690
Chromosome Location	chr2:141835116-141835117
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:141835054..141836662-chr2:141842749..141844903,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10167630	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs10168120	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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10496866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10496867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs10803480	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12464862	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12477423	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1357966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1404893	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473661	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1473663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525584	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525585	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1525589	0.87[YRI][hapmap]
rs1534128	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16845233	1.00[JPT][hapmap]
rs16845274	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1882642	0.82[CHB][hapmap]
rs1882643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1882644	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs1922701	0.81[ASN][1000 genomes]
rs1922709	0.82[CHB][hapmap]
rs2049478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs2049479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap]
rs2140872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2380965	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845638	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs3856355	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap]
rs3856358	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs4954689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4954691	0.87[YRI][hapmap]
rs4954880	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs6719409	0.86[YRI][hapmap]
rs6730194	0.83[ASN][1000 genomes]
rs6755234	0.82[CHB][hapmap]
rs7575215	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7601662	1.00[CHB][hapmap];0.89[JPT][hapmap]

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	nsv583198	chr2:141510791-142150620	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	nsv875211	chr2:141764693-141846346	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv875212	chr2:141796109-141877201	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv875213	chr2:141800473-141852429	Enhancers Active TSS Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv875214	chr2:141800473-141866271	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv875215	chr2:141800473-141877201	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv875216	chr2:141800473-141905052	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv875217	chr2:141800473-141919943	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv875218	chr2:141800473-141925845	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1003799	chr2:141803314-142033675	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv875219	chr2:141803602-141877201	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv459563	chr2:141803602-141925075	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv583200	chr2:141803602-141925075	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv875220	chr2:141819422-141882963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv875221	chr2:141826948-141877201	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv875222	chr2:141826948-141887814	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv875223	chr2:141826948-141905052	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv1009434	chr2:141832339-142156180	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv459574	chr2:141833621-141866271	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv583201	chr2:141833621-141866271	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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