Variant report

Variant	rs7602423
Chromosome Location	chr2:125844388-125844389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10167742	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10173995	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10178610	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10178941	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10188831	0.83[ASN][1000 genomes]
rs10192610	0.85[EUR][1000 genomes]
rs10201829	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11123079	0.83[ASN][1000 genomes]
rs11123081	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12328802	0.96[ASN][1000 genomes]
rs12466712	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12477887	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12619039	0.83[ASN][1000 genomes]
rs12711702	0.83[ASN][1000 genomes]
rs13393788	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13400338	0.96[ASN][1000 genomes]
rs1369525	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs314888	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs314889	0.83[ASN][1000 genomes]
rs314910	0.83[ASN][1000 genomes]
rs314912	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs314913	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs314914	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3924286	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4276033	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4359662	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4438483	0.83[ASN][1000 genomes]
rs4505537	1.00[CHB][hapmap]
rs4602234	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4622728	0.93[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs60640542	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6541980	0.87[EUR][1000 genomes]
rs6717901	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6722269	0.90[ASN][1000 genomes]
rs6755508	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6761589	0.87[EUR][1000 genomes]
rs7572346	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7587526	0.80[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	nsv874991	chr2:125692490-125901811	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv834362	chr2:125733921-125907451	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv431646	chr2:125780602-126174341	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv874992	chr2:125817682-126046421	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7602423	SFT2D3	cis	parietal	SCAN
rs7602423	WDR33	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:125843600-125844600	Enhancers	Fetal Intestine Large	intestine
2	chr2:125843800-125845000	Flanking Active TSS	Liver	Liver
3	chr2:125844000-125844400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:125844000-125844400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:125844000-125844600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr2:125844200-125844400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr2:125844200-125844800	Flanking Active TSS	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links