Variant report

Variant	rs2659639
Chromosome Location	chr12:58439226-58439227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs1027800	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747790	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783860	0.83[AMR][1000 genomes]
rs10783864	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10783865	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783866	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783867	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783868	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783873	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10877050	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10877052	0.80[EUR][1000 genomes]
rs10877053	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877055	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877056	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877065	0.88[ASN][1000 genomes]
rs10877066	0.90[ASN][1000 genomes]
rs10877067	0.90[ASN][1000 genomes]
rs11172419	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11172421	0.80[EUR][1000 genomes]
rs11172422	0.80[EUR][1000 genomes]
rs11172425	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172427	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172446	0.90[ASN][1000 genomes]
rs11172456	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11495521	0.86[ASN][1000 genomes]
rs11608939	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11615925	0.83[ASN][1000 genomes]
rs11615944	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11834786	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11834807	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12422985	0.80[EUR][1000 genomes]
rs12580381	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12820787	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12824706	0.92[ASN][1000 genomes]
rs1304496	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1354794	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1354795	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1395511	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1395514	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1466972	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1506883	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506885	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506888	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1506890	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1567130	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1580976	0.91[ASN][1000 genomes]
rs1580977	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1605329	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1605330	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1605331	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1605334	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1605335	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17120134	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17120179	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17120182	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1848129	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1857941	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1911258	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1911259	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1911260	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1911261	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1911262	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2002580	0.92[ASN][1000 genomes]
rs2089377	0.97[EUR][1000 genomes]
rs2102349	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2221541	0.80[EUR][1000 genomes]
rs2372376	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2372377	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2659641	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659646	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659659	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2659662	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2659665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2717404	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2720173	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2720176	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720178	0.94[EUR][1000 genomes]
rs2720179	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2720181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720191	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2888299	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34504532	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34885501	0.92[ASN][1000 genomes]
rs35195629	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35264128	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35403899	0.84[ASN][1000 genomes]
rs35599363	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36174144	0.82[ASN][1000 genomes]
rs3913866	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4257013	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4403837	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4435045	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4439558	0.85[ASN][1000 genomes]
rs4444117	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465402	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4489786	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4565944	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4575322	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760181	0.80[EUR][1000 genomes]
rs4760182	0.80[EUR][1000 genomes]
rs4760186	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760187	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760188	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760361	0.87[ASN][1000 genomes]
rs4760362	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760364	0.92[ASN][1000 genomes]
rs4760365	0.92[ASN][1000 genomes]
rs4760366	0.90[ASN][1000 genomes]
rs6581171	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6581173	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581177	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581178	0.87[ASN][1000 genomes]
rs7132168	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7135328	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7135728	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136458	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7139165	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71461350	0.82[ASN][1000 genomes]
rs7304458	0.80[EUR][1000 genomes]
rs7304628	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7304755	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7308860	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7309322	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7309793	0.87[ASN][1000 genomes]
rs7309912	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7314066	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954592	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7954914	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7959717	0.90[ASN][1000 genomes]
rs7963367	0.80[EUR][1000 genomes]
rs7970516	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7972562	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7978423	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7979813	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7980024	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7980627	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs871907	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs871908	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs951901	0.80[EUR][1000 genomes]
rs970249	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs982492	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs982493	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases
2	nsv899124	chr12:58391839-58883507	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2659639	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs2659639	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs2659639	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs2659639	XRCC6BP1	cis	Artery Tibial	GTEx
rs2659639	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs2659639	XRCC6BP1	cis	Whole Blood	GTEx
rs2659639	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs2659639	XRCC6BP1	cis	Thyroid	GTEx
rs2659639	XRCC6BP1	cis	Nerve Tibial	GTEx
rs2659639	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs2659639	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs2659639	XRCC6BP1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58433200-58439800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:58439200-58439400	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links