Variant report

Variant	rs1397683
Chromosome Location	chr4:152715916-152715917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10001603	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10013612	0.80[AMR][1000 genomes];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	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11099829	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11723227	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11932383	0.83[AMR][1000 genomes]
rs12502446	0.91[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];0.80[JPT][hapmap]
rs13108359	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13119490	0.99[AFR][1000 genomes];0.99[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];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13149588	0.83[AMR][1000 genomes]
rs1366907	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1429558	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1429559	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877185	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877186	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877188	0.89[CEU][hapmap]
rs2089811	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2175409	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303866	0.89[JPT][hapmap]
rs2406973	0.92[CEU][hapmap]
rs3805356	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3828546	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4399967	0.85[EUR][1000 genomes]
rs4554052	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4643789	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696110	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696290	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696295	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]
rs4696296	0.85[ASN][1000 genomes]
rs4696297	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58751443	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59350867	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61308159	0.85[EUR][1000 genomes]
rs62328980	0.84[EUR][1000 genomes]
rs6535816	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6535822	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6847844	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6849111	0.99[AFR][1000 genomes];0.88[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	0.80[AMR][1000 genomes];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];0.80[JPT][hapmap]
rs7669761	0.92[CEU][hapmap];0.80[JPT][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1397683	PET112L	cis	Lymphoblastoid	GTEx
rs1397683	PET112L	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links