Variant report

Variant	rs1878585
Chromosome Location	chr2:99501698-99501699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10169003	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10172158	0.94[EUR][1000 genomes]
rs10181972	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10188156	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11123755	0.94[EUR][1000 genomes]
rs11887536	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11893888	0.89[EUR][1000 genomes]
rs12468024	0.94[EUR][1000 genomes]
rs12474283	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12712035	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12712036	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs12712038	0.94[EUR][1000 genomes]
rs12712039	0.95[EUR][1000 genomes]
rs12712041	0.83[EUR][1000 genomes]
rs12712043	0.80[EUR][1000 genomes]
rs12992214	0.85[ASN][1000 genomes]
rs13004700	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs13004923	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011428	0.81[EUR][1000 genomes]
rs1356424	0.83[EUR][1000 genomes]
rs1568213	0.81[EUR][1000 genomes]
rs1581250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581251	0.94[EUR][1000 genomes]
rs1607256	0.80[EUR][1000 genomes]
rs17758170	0.81[CEU][hapmap]
rs1878589	0.81[CEU][hapmap]
rs1949424	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1983352	0.93[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2280256	0.91[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4263159	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs4850888	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4850889	0.83[EUR][1000 genomes]
rs4851162	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4851163	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4851167	0.94[EUR][1000 genomes]
rs4851170	0.94[EUR][1000 genomes]
rs4851171	0.94[EUR][1000 genomes]
rs4851173	0.83[EUR][1000 genomes]
rs4851177	0.84[EUR][1000 genomes]
rs6419564	0.84[EUR][1000 genomes]
rs6542838	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6542839	0.84[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs6542841	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs6542843	0.84[EUR][1000 genomes]
rs6711022	0.86[EUR][1000 genomes]
rs6713991	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6714243	0.94[EUR][1000 genomes]
rs6717372	0.92[EUR][1000 genomes]
rs6719634	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs6724477	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs6726156	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6739097	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6739176	0.84[EUR][1000 genomes]
rs6739503	0.83[EUR][1000 genomes]
rs6752025	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6757098	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs6760065	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs7423519	0.81[CEU][hapmap]
rs7579189	0.80[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7593332	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7608889	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs883773	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs925887	0.88[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs981601	0.80[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs981602	0.80[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.90[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1878585	FAHD2B	cis	parietal	SCAN
rs1878585	LIPT1	cis	parietal	SCAN
rs1878585	C2orf15	cis	parietal	SCAN
rs1878585	MAL	cis	parietal	SCAN
rs1878585	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:4 , 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	chr2:99501000-99502000	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links