Variant report

Variant	rs12639028
Chromosome Location	chr3:101346033-101346034
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101343899..101346704-chr3:101352292..101354517,2	K562	blood:
2	chr3:101343521..101346428-chr3:101395311..101397693,2	K562	blood:

Variant related genes	Relation type
ENSG00000066422	Chromatin interaction
ENSG00000256628	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1031710	0.80[EUR][1000 genomes]
rs1056579	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10936707	0.83[ASN][1000 genomes]
rs1138818	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11706986	0.82[EUR][1000 genomes]
rs11708845	0.84[ASN][1000 genomes]
rs11710533	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11711079	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11712748	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11715368	0.90[ASN][1000 genomes]
rs11717046	0.83[EUR][1000 genomes]
rs11720560	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11720745	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11914318	0.82[EUR][1000 genomes]
rs11917569	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11917682	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11919389	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11923273	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11924013	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11925001	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12629658	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629954	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12635128	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12636557	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13059470	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13061565	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13069443	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13077703	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13081846	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13082236	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13100262	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17345528	0.82[ASN][1000 genomes]
rs17345786	0.87[ASN][1000 genomes]
rs17411983	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17508319	0.87[ASN][1000 genomes]
rs1963961	0.80[EUR][1000 genomes]
rs2288272	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303474	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3094295	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3094296	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3094297	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3109756	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34301719	0.85[EUR][1000 genomes]
rs34624546	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34883763	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35117343	0.83[EUR][1000 genomes]
rs35850993	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36002990	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36060163	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3762729	0.84[ASN][1000 genomes]
rs3804775	0.84[ASN][1000 genomes]
rs3804778	0.82[ASN][1000 genomes]
rs3806653	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3806654	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3864012	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55654108	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55821257	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55859364	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56291106	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58907984	0.84[ASN][1000 genomes]
rs59596156	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62282218	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71625262	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73863360	0.87[ASN][1000 genomes]
rs7629753	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7645391	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7651406	0.94[EUR][1000 genomes]
rs7651721	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9830943	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs997739	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12639028	NXPE3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101344000-101348800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:101345600-101346200	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links