Variant report

Variant	rs56137970
Chromosome Location	chr5:59873462-59873463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10939857	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11739209	0.84[EUR][1000 genomes]
rs11739724	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11740327	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11745077	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11745627	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11747927	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11948543	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11951503	0.89[ASN][1000 genomes]
rs11951950	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11952735	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11956023	0.83[ASN][1000 genomes]
rs11959922	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1379116	0.87[ASN][1000 genomes]
rs1379117	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1445852	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs153152	0.82[ASN][1000 genomes]
rs1562235	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1816899	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1867702	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2061250	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2198865	0.85[ASN][1000 genomes]
rs248911	0.82[ASN][1000 genomes]
rs248912	0.82[ASN][1000 genomes]
rs249070	0.96[ASN][1000 genomes]
rs2591636	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs286148	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs286153	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs286154	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs286155	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs286156	0.85[ASN][1000 genomes]
rs286158	0.85[ASN][1000 genomes]
rs2898287	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34395679	0.85[EUR][1000 genomes]
rs3857236	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3958943	0.96[ASN][1000 genomes]
rs4353978	0.84[EUR][1000 genomes]
rs4538567	0.87[EUR][1000 genomes]
rs4699959	0.89[ASN][1000 genomes]
rs4700378	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700379	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700380	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4700381	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5012862	0.93[ASN][1000 genomes]
rs55720622	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55768631	0.96[ASN][1000 genomes]
rs56166952	0.91[ASN][1000 genomes]
rs56191602	0.85[ASN][1000 genomes]
rs59155887	0.84[ASN][1000 genomes]
rs62372964	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62373024	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62373025	0.82[EUR][1000 genomes]
rs6877561	0.85[ASN][1000 genomes]
rs6896942	0.92[ASN][1000 genomes]
rs7719726	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56137970	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59873000-59875200	Weak transcription	Pancreas	Pancrea
2	chr5:59873000-59908600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:59873000-59908800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:59873200-59881200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:59873200-59911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:59873400-59873600	Weak transcription	Dnd41	blood
7	chr5:59873400-59875000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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