Variant report

Variant	rs2433340
Chromosome Location	chr10:90160023-90160024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:89622921..89625081-chr10:90159029..90160699,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171862	Chromatin interaction
ENSG00000227268	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1067839	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1067840	1.00[CEU][hapmap];0.86[CHD][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10736351	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10736352	0.83[EUR][1000 genomes]
rs10749589	0.82[EUR][1000 genomes]
rs10749590	1.00[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs10749591	0.82[EUR][1000 genomes]
rs10788592	0.81[JPT][hapmap]
rs10788597	0.82[CHB][hapmap]
rs10788598	1.00[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs10788599	1.00[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs10788600	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10788602	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10887800	0.82[JPT][hapmap]
rs10887801	0.87[JPT][hapmap]
rs10887803	0.83[JPT][hapmap]
rs10887813	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10887817	0.92[CEU][hapmap]
rs10887818	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10887821	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10887823	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10887824	0.82[EUR][1000 genomes]
rs11202716	0.83[JPT][hapmap]
rs11202723	0.87[JPT][hapmap]
rs1342450	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1342451	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1342456	0.82[EUR][1000 genomes]
rs1346226	0.83[JPT][hapmap]
rs1426619	0.87[JPT][hapmap]
rs1617881	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1750274	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs1935579	1.00[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1935584	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2096194	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2185786	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs2312610	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2437875	0.80[CEU][hapmap]
rs2477956	0.96[CEU][hapmap]
rs2488270	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576170	0.80[CEU][hapmap]
rs2576171	0.80[CEU][hapmap]
rs2576172	0.80[CEU][hapmap]
rs2576181	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs2872092	0.81[EUR][1000 genomes]
rs4509673	0.82[EUR][1000 genomes]
rs4596981	0.81[EUR][1000 genomes]
rs4606392	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4619060	0.83[EUR][1000 genomes]
rs4933480	0.80[ASN][1000 genomes]
rs4934403	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4934404	1.00[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs4934409	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4934411	1.00[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6586129	0.80[JPT][hapmap]
rs6586132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6586134	0.92[CEU][hapmap]
rs6586139	0.82[EUR][1000 genomes]
rs7089911	0.83[JPT][hapmap]
rs7895582	0.85[JPT][hapmap]
rs7899828	0.81[EUR][1000 genomes]
rs7907732	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7909697	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7910594	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs7911996	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7917640	0.86[JPT][hapmap]
rs7918921	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7920126	0.81[JPT][hapmap]
rs7921352	0.96[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs792205	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs792207	0.92[CEU][hapmap];0.93[CHD][hapmap];0.81[EUR][1000 genomes]
rs792208	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs792209	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs792211	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792212	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs792213	0.92[CEU][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs792214	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792215	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs792230	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs792234	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs792235	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792236	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7922551	0.83[EUR][1000 genomes]
rs796945	0.84[CEU][hapmap]
rs806694	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs811558	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs813782	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs814242	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv1796143	chr10:90156447-90168074	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2433340	LIPA	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90156000-90161600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:90159400-90164400	Weak transcription	Fetal Lung	lung
3	chr10:90159800-90172800	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links