Variant report

Variant	rs12516488
Chromosome Location	chr5:45203199-45203200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12055286	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12153053	0.83[AMR][1000 genomes]
rs12153189	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12514414	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12514615	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12517546	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12520430	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521953	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12522524	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12522910	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12523384	0.92[ASN][1000 genomes]
rs1472584	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16902068	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16902083	0.80[ASN][1000 genomes]
rs4267876	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4308490	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4357042	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4493682	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4533895	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4566805	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367468	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367469	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367470	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62367473	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367515	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62367516	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62367520	0.80[ASN][1000 genomes]
rs62367522	0.80[ASN][1000 genomes]
rs62369907	0.81[AMR][1000 genomes]
rs62369908	0.81[AMR][1000 genomes]
rs62369910	0.81[AMR][1000 genomes]
rs62369912	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62369916	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62369917	0.92[ASN][1000 genomes]
rs6881773	0.81[EUR][1000 genomes]
rs6898476	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7703487	0.81[EUR][1000 genomes]
rs7711444	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7711446	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7711528	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7720104	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033740	chr5:44996257-45378556	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv537743	chr5:44996257-45378556	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1018651	chr5:45003750-45437670	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv537744	chr5:45003750-45437670	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv869151	chr5:45003751-45362364	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv830280	chr5:45067773-45250757	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv2760956	chr5:45180567-45220336	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv532804	chr5:45184041-45972996	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv1800833	chr5:45191744-45229673	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	esv1799409	chr5:45191744-45249604	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv2422014	chr5:45192192-45212691	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv597966	chr5:45192314-45205747	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv597967	chr5:45192314-45210282	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv597970	chr5:45192384-45234541	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12516488	LOC647121	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:45200000-45205600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links