Variant report

Variant	rs57489086
Chromosome Location	chr2:114550308-114550309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11685086	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11692142	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870303	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3982388	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849276	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56884727	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58511785	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59123894	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60221109	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62170104	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62170106	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62170136	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72946678	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7567042	0.85[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs57489086	DDX11L2	cis	lung	GTEx
rs57489086	RPL23AP7	cis	lung	GTEx
rs57489086	RPL23AP7	cis	Artery Aorta	GTEx
rs57489086	DDX11L2	cis	Muscle Skeletal	GTEx
rs57489086	DDX11L2	cis	Adipose Subcutaneous	GTEx
rs57489086	DDX11L2	cis	Whole Blood	GTEx
rs57489086	RPL23AP7	cis	Artery Tibial	GTEx
rs57489086	RPL23AP7	cis	Whole Blood	GTEx
rs57489086	RPL23AP7	cis	Heart Left Ventricle	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114549000-114550400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:114549200-114550400	Enhancers	Fetal Kidney	kidney
3	chr2:114549800-114550400	Enhancers	Primary B cells from cord blood	blood
4	chr2:114549800-114550400	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:114550000-114550800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:114550000-114552400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:114550000-114552600	Weak transcription	Fetal Intestine Small	intestine
8	chr2:114550000-114552800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:114550000-114552800	Weak transcription	HSMM	muscle
10	chr2:114550000-114557000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:114550200-114550600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:114550200-114550600	Enhancers	GM12878-XiMat	blood
13	chr2:114550200-114552400	Weak transcription	Fetal Intestine Large	intestine
14	chr2:114550200-114552400	Weak transcription	A549	lung
15	chr2:114550200-114552400	Weak transcription	Osteobl	bone
16	chr2:114550200-114552600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:114550200-114552600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:114550200-114552600	Weak transcription	NHLF	lung
19	chr2:114550200-114553000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:114550200-114555800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:114550200-114563800	Weak transcription	Rectal Mucosa Donor 29	rectum

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