Variant report

Variant	rs12613159
Chromosome Location	chr2:114554932-114554933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10167730	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177576	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10179657	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10209330	0.88[ASN][1000 genomes]
rs10496453	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123207	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11686297	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11694130	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12711788	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17040397	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2122097	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2442136	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2595140	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2595152	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2687623	0.84[ASN][1000 genomes]
rs2687624	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2687626	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2687627	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2687628	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687630	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28451366	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34332133	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35734534	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4848349	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4848350	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4849275	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4849277	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4849278	0.85[ASN][1000 genomes]
rs4849279	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6711542	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7600228	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12613159	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs12613159	RPL23AP7	cis	Whole Blood	GTEx
rs12613159	RPL23AP7	cis	Artery Tibial	GTEx
rs12613159	DDX11L2	cis	Whole Blood	GTEx
rs12613159	RPL23AP7	cis	Esophagus Muscularis	GTEx
rs12613159	RPL23AP7	cis	Muscle Skeletal	GTEx
rs12613159	RPL23AP7	cis	Artery Aorta	GTEx
rs12613159	RPL23AP7	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114550000-114557000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:114550200-114555800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:114550200-114563800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:114552800-114555000	Enhancers	Duodenum Mucosa	Duodenum
5	chr2:114553200-114557200	Weak transcription	Osteobl	bone
6	chr2:114553600-114557200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:114553800-114556600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:114554400-114555200	Weak transcription	Fetal Intestine Small	intestine
9	chr2:114554600-114564400	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links