Variant report

Variant	rs56699889
Chromosome Location	chr5:45125618-45125619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12054976	0.90[AMR][1000 genomes]
rs12055286	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12153053	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12153189	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12514414	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12515179	0.82[ASN][1000 genomes]
rs12520430	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12523384	0.86[ASN][1000 genomes]
rs1472584	0.86[EUR][1000 genomes]
rs4267876	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4308490	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4357042	0.86[EUR][1000 genomes]
rs4493682	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4533895	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4566805	0.86[EUR][1000 genomes]
rs59468706	0.82[AMR][1000 genomes]
rs62367468	0.86[EUR][1000 genomes]
rs62367469	0.86[EUR][1000 genomes]
rs62367470	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62367473	0.84[EUR][1000 genomes]
rs62369894	0.82[AMR][1000 genomes]
rs62369895	0.82[AMR][1000 genomes]
rs62369896	0.82[AMR][1000 genomes]
rs62369905	0.88[AMR][1000 genomes]
rs62369907	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62369908	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62369910	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62369912	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62369913	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62369916	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62369917	0.86[ASN][1000 genomes]
rs6881773	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6898476	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7701679	0.90[AMR][1000 genomes]
rs7703487	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7711444	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7711446	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7711528	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7716101	0.84[AMR][1000 genomes]
rs7720104	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56699889	LOC647121	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:45124400-45126000	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr5:45125400-45126000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr5:45125600-45126000	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links