Variant report

Variant	rs2970582
Chromosome Location	chr1:212080831-212080832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10158561	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10465691	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs10863930	0.86[EUR][1000 genomes]
rs10863932	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11119806	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs11119821	0.82[ASN][1000 genomes]
rs11119822	0.86[EUR][1000 genomes]
rs12038038	0.80[CEU][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs1539195	0.80[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs2002081	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788119	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788120	0.96[ASN][1000 genomes]
rs2788123	0.81[EUR][1000 genomes]
rs2788124	0.94[CHB][hapmap]
rs2788126	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2788127	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2788132	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2788143	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2788147	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808378	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2808379	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2970587	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2998418	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795834	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4480424	0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4951425	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4951431	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4951434	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4951550	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4951552	0.80[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs4951553	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6540712	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6680326	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6685247	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698841	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7515713	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7518285	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7518833	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7522107	0.84[ASN][1000 genomes]
rs7533928	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533951	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs947438	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9651110	0.83[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762218	chr1:212046447-212087682	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
2	esv3527308	chr1:212079479-212082377	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
3	esv3452684	chr1:212080132-212081517	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
4	esv3527306	chr1:212080249-212081358	Enhancers Weak transcription	lncRNA	n/a	inside rSNPs	n/a
5	esv3452685	chr1:212080253-212081356	Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	n/a
6	esv3527309	chr1:212080253-212081356	Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2970582	LPGAT1	cis	cerebellum	SCAN
rs2970582	RD3	cis	cerebellum	SCAN
rs2970582	RCOR3	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212076200-212083600	Weak transcription	Pancreas	Pancrea
2	chr1:212077200-212082600	Weak transcription	Colonic Mucosa	Colon
3	chr1:212077400-212082400	Weak transcription	Adipose Nuclei	Adipose
4	chr1:212078000-212082400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:212078000-212082400	Weak transcription	HepG2	liver
6	chr1:212078400-212081800	Weak transcription	Liver	Liver
7	chr1:212079600-212087400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:212080000-212081000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr1:212080400-212087600	Enhancers	Fetal Intestine Large	intestine
10	chr1:212080800-212081000	Enhancers	Esophagus	oesophagus
11	chr1:212080800-212081400	Enhancers	GM12878-XiMat	blood
12	chr1:212080800-212087000	Enhancers	Fetal Intestine Small	intestine

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