Variant report

Variant	rs12613610
Chromosome Location	chr2:86897501-86897502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86848186..86849985-chr2:86897353..86900305,2	MCF-7	breast:
2	chr2:86895644..86897358-chr2:86897383..86900357,2	MCF-7	breast:
3	chr2:86849384..86851412-chr2:86897140..86899162,2	MCF-7	breast:
4	chr2:86856951..86859444-chr2:86896714..86898569,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249884	Chromatin interaction
ENSG00000239305	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1005834	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs10165914	0.90[ASN][1000 genomes]
rs10178968	0.90[ASN][1000 genomes]
rs10184617	0.87[ASN][1000 genomes]
rs10186663	0.86[CEU][hapmap]
rs10197478	0.90[ASN][1000 genomes]
rs10201422	0.81[CEU][hapmap]
rs10206802	0.90[ASN][1000 genomes]
rs1049457	0.81[CEU][hapmap]
rs1049458	0.81[CEU][hapmap]
rs11127049	0.88[ASN][1000 genomes]
rs1193	0.81[CEU][hapmap]
rs12623395	0.80[JPT][hapmap]
rs12988718	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13407663	0.90[ASN][1000 genomes]
rs1370452	0.90[ASN][1000 genomes]
rs1850138	0.81[CEU][hapmap]
rs1878109	0.86[CEU][hapmap]
rs2063848	0.85[CEU][hapmap]
rs2138396	0.86[CEU][hapmap]
rs2138397	0.86[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2367378	0.81[CEU][hapmap]
rs2887012	0.86[CEU][hapmap]
rs308920	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs308921	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36100635	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4832047	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832048	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4832306	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832311	0.86[CEU][hapmap]
rs59818518	0.85[ASN][1000 genomes]
rs6547701	0.90[ASN][1000 genomes]
rs6711700	0.81[ASN][1000 genomes]
rs6726451	0.81[CEU][hapmap]
rs6731890	0.86[CEU][hapmap]
rs6743139	0.86[MEX][hapmap]
rs72934456	0.90[ASN][1000 genomes]
rs72934463	0.88[ASN][1000 genomes]
rs72934466	0.90[ASN][1000 genomes]
rs7558827	0.80[CHB][hapmap]
rs7564251	0.90[ASN][1000 genomes]
rs9309636	0.86[CEU][hapmap]
rs9309637	0.86[CEU][hapmap]
rs9309638	0.86[CEU][hapmap]
rs9808243	0.90[ASN][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	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv829489	chr2:86896770-86899157	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12613610	PLGLB1	cis	multi-tissue	Pritchard
rs12613610	SEC22A	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86888800-86898200	Weak transcription	Ovary	ovary
2	chr2:86891800-86898600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:86892000-86901200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:86897400-86897600	Enhancers	A549	lung
5	chr2:86897400-86897800	Enhancers	Rectal Smooth Muscle	rectum
6	chr2:86897400-86899000	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links