Variant report

Variant	rs2312193
Chromosome Location	chr3:141188399-141188400
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	chr3:141186500..141188582-chr3:141205039..141207172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11711375	0.96[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes]
rs11917587	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs13069717	0.87[EUR][1000 genomes]
rs1366042	0.96[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1493209	0.92[CEU][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs1493210	0.88[ASN][1000 genomes]
rs1582875	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16851438	0.83[JPT][hapmap]
rs16851441	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16851483	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1863867	0.88[JPT][hapmap]
rs2035935	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2035936	0.83[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2042864	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs2639997	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2640017	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs295299	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs295300	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs295320	0.92[CEU][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs295321	0.88[ASN][1000 genomes]
rs295323	0.89[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap]
rs295324	0.88[ASN][1000 genomes]
rs34558081	0.92[ASN][1000 genomes]
rs35711802	0.87[EUR][1000 genomes]
rs3732869	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3806646	0.92[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes]
rs3806648	0.91[ASN][1000 genomes]
rs3821709	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3821710	0.92[CEU][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs3821712	0.92[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs4683404	0.88[JPT][hapmap]
rs4683610	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs58025624	0.88[ASN][1000 genomes]
rs60654199	0.81[ASN][1000 genomes]
rs62282002	0.83[ASN][1000 genomes]
rs6763498	0.86[EUR][1000 genomes]
rs6767158	0.92[CEU][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.88[EUR][1000 genomes]
rs6776003	0.82[CEU][hapmap]
rs6785874	0.92[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.87[EUR][1000 genomes]
rs6795168	0.92[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6800122	0.92[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.87[EUR][1000 genomes]
rs6808837	0.92[CEU][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.87[EUR][1000 genomes]
rs73871847	0.86[ASN][1000 genomes]
rs7626871	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7627774	0.92[ASN][1000 genomes]
rs7627807	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7632308	0.92[CEU][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7643837	0.92[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.87[EUR][1000 genomes]
rs9289630	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9289631	0.86[EUR][1000 genomes]
rs9813177	0.92[CEU][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9851256	0.82[CEU][hapmap]
rs9878347	0.83[JPT][hapmap]
rs9879503	0.83[JPT][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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv965217	chr3:141184266-141190303	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv3418672	chr3:141188094-141188488	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2312193	ZBTB38	cis	cerebellum	SCAN
rs2312193	RASA2	cis	parietal	SCAN
rs2312193	GK5	cis	parietal	SCAN
rs2312193	ATP1B3	cis	cerebellum	SCAN
rs2312193	RASA2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141177000-141189600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:141184400-141188800	Weak transcription	NH-A	brain
3	chr3:141184400-141189600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:141184600-141189600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:141184600-141189800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:141184600-141201000	Weak transcription	NHLF	lung
7	chr3:141188200-141189200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:141188200-141190400	Enhancers	Osteobl	bone
9	chr3:141188200-141190800	Enhancers	NHDF-Ad	bronchial

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