Variant report

Variant	rs10209398
Chromosome Location	chr2:151151095-151151096
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	chr2:151135439..151137245-chr2:151148453..151151418,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10165225	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10165666	1.00[EUR][1000 genomes]
rs10173947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1036793	0.83[EUR][1000 genomes]
rs11693655	1.00[EUR][1000 genomes]
rs11888189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11895581	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11899312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12623971	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12692649	1.00[EUR][1000 genomes]
rs13394286	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1372431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1372432	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1372433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1372435	0.83[EUR][1000 genomes]
rs1372436	0.83[EUR][1000 genomes]
rs1441969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1441970	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16828061	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16828069	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1899375	0.83[EUR][1000 genomes]
rs1978941	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2334315	0.83[EUR][1000 genomes]
rs35956280	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36025659	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs3924622	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4233802	1.00[EUR][1000 genomes]
rs4299356	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4362583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4366927	0.97[EUR][1000 genomes]
rs4402789	1.00[EUR][1000 genomes]
rs4404295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4414701	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4425094	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4425095	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4491744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4508619	1.00[EUR][1000 genomes]
rs4522630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4544461	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4563247	1.00[EUR][1000 genomes]
rs4566385	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4577299	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4585053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4589784	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4589785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4600678	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4603783	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4606957	1.00[EUR][1000 genomes]
rs4664428	0.83[EUR][1000 genomes]
rs62167367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62167368	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs62167369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6727491	0.83[EUR][1000 genomes]
rs6731304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6740399	0.83[EUR][1000 genomes]
rs6748737	1.00[EUR][1000 genomes]
rs6761282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6761697	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs734135	0.83[EUR][1000 genomes]
rs7560459	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7563730	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7564257	1.00[EUR][1000 genomes]
rs7564743	1.00[EUR][1000 genomes]
rs7608140	0.92[EUR][1000 genomes]
rs7608904	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9287819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9287820	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995119	chr2:150556150-151294696	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10209398	HBG2	trans	brain	seeQTL
rs10209398	HBG1	trans	brain	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151143200-151151600	Weak transcription	Aorta	Aorta
2	chr2:151143800-151153000	Weak transcription	NHDF-Ad	bronchial
3	chr2:151149400-151151200	Enhancers	HMEC	breast
4	chr2:151150000-151151200	Enhancers	NHEK	skin
5	chr2:151150000-151152200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:151150800-151153200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:151151000-151153200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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