Variant report

Variant	rs1479858
Chromosome Location	chr3:140098286-140098287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140096590..140099574-chr3:140099849..140101936,2	K562	blood:
2	chr3:140093026..140095347-chr3:140098280..140100023,2	K562	blood:
3	chr3:140087589..140090297-chr3:140098054..140099606,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10212107	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10212135	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10212140	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs1026780	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10804672	0.99[AFR][1000 genomes]
rs10804673	0.88[AFR][1000 genomes]
rs1159437	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11916924	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11927470	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13088193	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1319583	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1383017	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1383018	1.00[YRI][hapmap]
rs1479853	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1479854	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1479855	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1479859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1479860	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1479861	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1479862	1.00[EUR][1000 genomes]
rs1585817	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1600401	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1904486	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1993960	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1993961	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2127471	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2127472	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3903534	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3943278	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4368463	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4393867	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4589894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4638925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4683489	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4683490	1.00[EUR][1000 genomes]
rs4683823	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4683827	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683828	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769101	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6769574	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6773289	1.00[CEU][hapmap];0.83[MKK][hapmap];1.00[EUR][1000 genomes]
rs6786062	1.00[CEU][hapmap];0.98[MKK][hapmap];1.00[EUR][1000 genomes]
rs6797439	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804095	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs899623	1.00[EUR][1000 genomes]
rs899624	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs931123	1.00[CEU][hapmap];0.87[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs931124	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs931125	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs931126	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9828897	1.00[CEU][hapmap];0.83[MKK][hapmap];1.00[EUR][1000 genomes]
rs9839825	1.00[CEU][hapmap]
rs9877035	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv829740	chr3:139925767-140106169	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv460867	chr3:140007294-140180563	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv591861	chr3:140007294-140180563	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv818169	chr3:140014763-140182046	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1001430	chr3:140016999-140186498	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv998953	chr3:140017168-140186984	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv536731	chr3:140017168-140186984	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv829741	chr3:140021063-140183294	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1004500	chr3:140021594-140189148	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140087600-140104600	Weak transcription	Brain Angular Gyrus	brain
2	chr3:140090000-140105400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:140092800-140104600	Weak transcription	Right Atrium	heart
4	chr3:140095800-140099600	Weak transcription	Ovary	ovary
5	chr3:140096200-140105200	Weak transcription	Esophagus	oesophagus
6	chr3:140097000-140098400	Enhancers	HSMM	muscle
7	chr3:140097200-140098400	Enhancers	HSMMtube	muscle
8	chr3:140097400-140098400	Enhancers	NH-A	brain
9	chr3:140097600-140098400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr3:140098200-140098400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links