Variant report

Variant	rs6453403
Chromosome Location	chr5:70680532-70680533
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 47 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4704274	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59966095	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6453405	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6453406	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7378507	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529287	chr5:69732192-70716662	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1033366	chr5:70254883-70710447	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv882135	chr5:70275720-70689452	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv980680	chr5:70530575-70702151	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv882173	chr5:70567610-70689452	Weak transcription Enhancers Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv882175	chr5:70576973-70689452	Enhancers Weak transcription Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1018141	chr5:70654060-70708985	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1031941	chr5:70654060-70710447	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1017385	chr5:70660739-70710447	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv1850052	chr5:70674583-70745387	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv528571	chr5:70679626-70767269	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:47)

SNP	Gene	Cis/trans	Tissue	Source
rs6453403	RP11-195E2.4	cis	Stomach	GTEx
rs6453403	RP11-195E2.1	cis	Esophagus Muscularis	GTEx
rs6453403	RP11-195E2.4	cis	Adipose Subcutaneous	GTEx
rs6453403	GTF2H2B	cis	Muscle Skeletal	GTEx
rs6453403	RP11-195E2.1	cis	lung	GTEx
rs6453403	RP11-195E2.4	cis	Artery Aorta	GTEx
rs6453403	RP11-497H16.2	cis	Artery Tibial	GTEx
rs6453403	RP11-195E2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs6453403	RP11-136K7.2	cis	Esophagus Muscularis	GTEx
rs6453403	RP11-195E2.1	cis	Whole Blood	GTEx
rs6453403	RP11-195E2.4	cis	Esophagus Mucosa	GTEx
rs6453403	RP11-589F5.3	cis	Whole Blood	GTEx
rs6453403	RP11-497H16.2	cis	Esophagus Muscularis	GTEx
rs6453403	RP11-195E2.4	cis	Thyroid	GTEx
rs6453403	RP11-195E2.1	cis	Adipose Subcutaneous	GTEx
rs6453403	LOC653080	trans	multi-tissue	Pritchard
rs6453403	RP11-497H16.2	cis	Esophagus Mucosa	GTEx
rs6453403	RP11-497H16.2	cis	Whole Blood	GTEx
rs6453403	LOC153561	cis	multi-tissue	Pritchard
rs6453403	GUSBL1	trans	multi-tissue	Pritchard
rs6453403	RP11-195E2.4	cis	Nerve Tibial	GTEx
rs6453403	RP11-195E2.4	cis	Heart Left Ventricle	GTEx
rs6453403	RP11-497H16.7	cis	Whole Blood	GTEx
rs6453403	RP11-195E2.4	cis	Esophagus Muscularis	GTEx
rs6453403	RP11-497H16.2	cis	Adipose Subcutaneous	GTEx
rs6453403	RP11-195E2.4	cis	Muscle Skeletal	GTEx
rs6453403	RP11-195E2.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6453403	RP11-497H16.4	cis	Whole Blood	GTEx
rs6453403	RP11-195E2.1	cis	Artery Aorta	GTEx
rs6453403	RP11-195E2.1	cis	Artery Tibial	GTEx
rs6453403	RP11-195E2.1	cis	Heart Left Ventricle	GTEx
rs6453403	RP11-195E2.1	cis	Muscle Skeletal	GTEx
rs6453403	RP11-195E2.4	cis	lung	GTEx
rs6453403	RP11-195E2.1	cis	Thyroid	GTEx
rs6453403	RP11-497H16.2	cis	Thyroid	GTEx
rs6453403	DKFZP686M0199	N/A	lymphoblastoid	RTeQTL
rs6453403	SMA5	cis	multi-tissue	Pritchard
rs6453403	RP11-195E2.4	cis	Artery Tibial	GTEx
rs6453403	RP11-195E2.4	cis	Whole Blood	GTEx
rs6453403	GTF2H2B	cis	Skin Sun Exposed Lower leg	GTEx
rs6453403	GTF2H2	cis	Whole Blood	GTEx
rs6453403	GTF2H2B	cis	Nerve Tibial	GTEx
rs6453403	LOC441081	cis	multi-tissue	Pritchard
rs6453403	GTF2H2	cis	lung	GTEx
rs6453403	RP11-195E2.1	cis	Nerve Tibial	GTEx
rs6453403	RP11-497H16.2	cis	Nerve Tibial	GTEx
rs6453403	RP11-497H16.2	cis	lung	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70680000-70681000	Enhancers	K562	blood
2	chr5:70680200-70680600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links