Variant report

Variant	rs4696295
Chromosome Location	chr4:152717430-152717431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10001603	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10013612	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10016160	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10222838	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10222925	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11099828	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11099829	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11723227	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11932383	0.82[AMR][1000 genomes]
rs12331037	0.81[GIH][hapmap]
rs12502446	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12503677	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12641433	0.92[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap]
rs13108359	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13119490	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13121178	0.88[EUR][1000 genomes]
rs13121190	0.84[EUR][1000 genomes]
rs13139327	0.85[EUR][1000 genomes]
rs13145446	0.88[EUR][1000 genomes]
rs13147021	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13149588	0.82[AMR][1000 genomes]
rs1366907	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1397683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1429558	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1429559	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17360475	0.81[GIH][hapmap]
rs1877185	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877186	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877188	0.88[CEU][hapmap]
rs2089811	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2175409	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303866	0.88[JPT][hapmap]
rs2406973	0.92[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs3805356	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3828546	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4399967	0.85[EUR][1000 genomes]
rs4554052	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4643789	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696109	0.81[GIH][hapmap]
rs4696110	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696290	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696293	0.85[GIH][hapmap]
rs4696296	0.85[ASN][1000 genomes]
rs4696297	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58751443	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59350867	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61308159	0.85[EUR][1000 genomes]
rs62328980	0.84[EUR][1000 genomes]
rs6535816	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6535818	0.81[GIH][hapmap]
rs6535819	0.81[GIH][hapmap]
rs6535822	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6847844	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6849111	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6855883	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6857073	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7654294	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7669465	0.92[CEU][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap]
rs7669761	0.92[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap]
rs7669977	0.81[GIH][hapmap]
rs7675818	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs867800	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9996320	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4696295	PET112L	cis	Lymphoblastoid	GTEx
rs4696295	PET112L	cis	cerebellum	SCAN
rs4696295	PET112L	cis	multi-tissue	Pritchard
rs4696295	FAM160A1	cis	cerebellum	SCAN
rs4696295	PET112L	cis	lymphoblastoid	seeQTL
rs4696295	PET112L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152708000-152717600	Weak transcription	Fetal Intestine Small	intestine
2	chr4:152711000-152720000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:152712600-152720200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:152714200-152719200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr4:152714400-152718000	Weak transcription	Fetal Heart	heart
6	chr4:152717200-152721200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr4:152717400-152717600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:152717400-152718000	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr4:152717400-152721600	Enhancers	Stomach Mucosa	stomach

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