Variant report

Variant	rs1581249
Chromosome Location	chr2:99500630-99500631
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99495810..99498238-chr2:99499497..99501291,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10175560	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11123756	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11900176	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11900524	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12467504	0.87[EUR][1000 genomes]
rs12474283	0.80[CEU][hapmap]
rs12478574	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12712033	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs12712034	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs12712037	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12712039	0.95[ASN][1000 genomes]
rs12712040	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12990579	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13004700	0.80[CEU][hapmap]
rs13005124	0.91[CEU][hapmap]
rs13005148	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13006398	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13024838	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13028500	0.91[CEU][hapmap]
rs17758170	0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[EUR][1000 genomes]
rs1878589	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1949424	0.89[EUR][1000 genomes]
rs1962029	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4311103	0.88[CEU][hapmap]
rs4499468	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4553869	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851174	0.87[CEU][hapmap]
rs4851175	0.91[CEU][hapmap]
rs6542841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6704682	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724477	0.96[CEU][hapmap]
rs6741166	0.91[EUR][1000 genomes]
rs6752025	0.90[EUR][1000 genomes]
rs6757098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6760065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7423519	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7565510	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565614	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7565736	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7565819	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7588441	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7590596	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7593332	0.89[EUR][1000 genomes]
rs7608889	0.81[CEU][hapmap]
rs883773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925887	0.87[CEU][hapmap]

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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99496800-99501800	Enhancers	Esophagus	oesophagus
2	chr2:99497800-99505600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:99500000-99517000	Weak transcription	Gastric	stomach
4	chr2:99500400-99500800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:99500400-99500800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr2:99500600-99501000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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