Variant report

Variant	rs5762870
Chromosome Location	chr22:29261159-29261160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1065497	0.84[ASN][1000 genomes]
rs12165962	0.88[ASW][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs1318025	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1318026	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs132528	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs132529	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs132531	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs132533	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs132536	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs132543	0.89[EUR][1000 genomes]
rs132548	0.87[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2015500	0.91[EUR][1000 genomes]
rs2064261	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2097461	0.89[JPT][hapmap]
rs2213645	0.95[JPT][hapmap]
rs2239815	0.89[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs2239828	0.83[CEU][hapmap]
rs2269577	0.89[JPT][hapmap]
rs2347447	0.89[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs3788409	0.89[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs469990	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs469991	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs469992	0.88[EUR][1000 genomes]
rs4822998	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs5752807	0.81[EUR][1000 genomes]
rs5752809	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs5752812	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs5752813	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5752826	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762784	0.89[JPT][hapmap];0.82[MEX][hapmap]
rs5762788	0.89[JPT][hapmap];0.91[MEX][hapmap]
rs5762795	0.88[ASW][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap]
rs5762824	0.81[EUR][1000 genomes]
rs5762825	0.81[EUR][1000 genomes]
rs5762854	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5762865	0.85[AMR][1000 genomes]
rs5762874	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762877	0.87[ASN][1000 genomes]
rs5762880	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5762881	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762882	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5762936	0.95[JPT][hapmap]
rs5997408	0.89[JPT][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5997412	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6005881	0.88[ASW][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap]
rs6005915	0.95[JPT][hapmap];0.86[MEX][hapmap]
rs6005916	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6005936	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6519766	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs715531	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7287806	0.94[ASW][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes]
rs7287918	0.83[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs763073	0.89[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs8137262	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8137969	0.81[EUR][1000 genomes]
rs8142067	0.86[EUR][1000 genomes]
rs9620841	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9625619	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5762870	GAL3ST1	cis	cerebellum	SCAN
rs5762870	ZNRF3	cis	parietal	SCAN
rs5762870	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs5762870	XBP1	cis	cerebellum	SCAN
rs5762870	MN1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29260200-29261200	Enhancers	Liver	Liver
2	chr22:29260400-29261800	Enhancers	Gastric	stomach
3	chr22:29260400-29261800	Enhancers	Pancreas	Pancrea
4	chr22:29260400-29262000	Flanking Active TSS	HepG2	liver
5	chr22:29260600-29261400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr22:29260600-29261600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr22:29260600-29261800	Enhancers	A549	lung
8	chr22:29260800-29261600	Enhancers	Lung	lung
9	chr22:29260800-29261800	Enhancers	Fetal Intestine Large	intestine
10	chr22:29260800-29261800	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr22:29260800-29261800	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr22:29261000-29261600	Enhancers	Duodenum Mucosa	Duodenum
13	chr22:29261000-29261600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr22:29261000-29261600	Enhancers	Stomach Mucosa	stomach
15	chr22:29261000-29261800	Enhancers	Fetal Intestine Small	intestine

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