Variant report

Variant	rs17029163
Chromosome Location	chr4:100502507-100502508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10007794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10008896	0.97[ASN][1000 genomes]
rs10008928	0.97[ASN][1000 genomes]
rs10013868	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10013883	0.87[ASN][1000 genomes]
rs10020461	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10022775	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10026790	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10030937	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10516443	0.91[ASN][1000 genomes]
rs10516444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1054730	0.94[ASN][1000 genomes]
rs1057615	1.00[ASN][1000 genomes]
rs11097668	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11933250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11933337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs11933937	1.00[ASN][1000 genomes]
rs11934921	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11935423	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11935581	0.97[ASN][1000 genomes]
rs11937107	1.00[ASN][1000 genomes]
rs11937273	1.00[ASN][1000 genomes]
rs11943031	1.00[ASN][1000 genomes]
rs11944749	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944750	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11944752	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];1.00[ASN][1000 genomes]
rs11946292	0.94[ASN][1000 genomes]
rs11946367	1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[ASN][1000 genomes]
rs11946658	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11947558	1.00[ASN][1000 genomes]
rs1503777	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17531824	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17598226	1.00[ASN][1000 genomes]
rs1800591	1.00[ASN][1000 genomes]
rs1800804	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2255119	0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2637768	0.95[ASN][1000 genomes]
rs2718684	0.95[ASN][1000 genomes]
rs28368786	1.00[ASN][1000 genomes]
rs28376611	1.00[ASN][1000 genomes]
rs28431971	0.94[ASN][1000 genomes]
rs28435607	1.00[ASN][1000 genomes]
rs28444681	0.88[ASN][1000 genomes]
rs28473262	1.00[ASN][1000 genomes]
rs28497720	1.00[ASN][1000 genomes]
rs28500697	0.97[ASN][1000 genomes]
rs2851225	0.95[ASN][1000 genomes]
rs28595160	1.00[ASN][1000 genomes]
rs28608631	0.97[ASN][1000 genomes]
rs28621060	0.97[ASN][1000 genomes]
rs28647519	1.00[ASN][1000 genomes]
rs2866164	1.00[ASN][1000 genomes]
rs28666735	0.98[ASN][1000 genomes]
rs28678377	0.97[ASN][1000 genomes]
rs28704064	1.00[ASN][1000 genomes]
rs28789770	1.00[ASN][1000 genomes]
rs28849180	1.00[ASN][1000 genomes]
rs2903201	0.94[ASN][1000 genomes]
rs3816873	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3817083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4423880	0.88[ASN][1000 genomes]
rs45440196	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6815231	0.89[ASN][1000 genomes]
rs6815416	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825248	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6839296	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6841211	0.93[ASN][1000 genomes]
rs6841282	0.91[ASN][1000 genomes]
rs6854911	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72681967	0.88[ASN][1000 genomes]
rs7656665	1.00[ASN][1000 genomes]
rs7661656	0.91[ASN][1000 genomes]
rs7661964	1.00[ASN][1000 genomes]
rs7682548	1.00[ASN][1000 genomes]
rs7686425	0.91[ASN][1000 genomes]
rs7687762	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7693203	1.00[ASN][1000 genomes]
rs9307240	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9997840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv933074	chr4:100460951-100630600	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1833664	chr4:100495571-100504985	Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17029163	ADH4	cis	parietal	SCAN
rs17029163	MTTP	cis	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100497400-100502800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr4:100497400-100505800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:100498200-100503000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:100500400-100503000	Weak transcription	HepG2	liver
5	chr4:100501800-100502800	Active TSS	Duodenum Mucosa	Duodenum
6	chr4:100502000-100507800	Genic enhancers	Liver	Liver
7	chr4:100502200-100503000	Weak transcription	Fetal Intestine Large	intestine
8	chr4:100502200-100503000	Weak transcription	Fetal Intestine Small	intestine

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