Variant report

Variant	rs2221541
Chromosome Location	chr12:58402465-58402466
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	chr12:58396203..58397967-chr12:58401267..58403984,2	K562	blood:

Extended variants
information (count: 168 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:165)

rs_ID	r²[population]
rs10506393	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747790	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10783864	0.83[ASN][1000 genomes]
rs10783865	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10783866	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10783867	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10783868	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10783873	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10877048	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877050	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877053	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10877055	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10877056	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10877065	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10877066	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10877067	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11172408	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172418	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172419	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172420	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172421	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172422	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172425	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172427	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172446	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11172456	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11608333	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11608939	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11615925	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11615944	0.85[AMR][1000 genomes]
rs11615959	0.80[AMR][1000 genomes]
rs11834786	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11834807	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12366757	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12366794	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12368024	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12580381	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12820787	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12824706	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12825843	0.83[EUR][1000 genomes]
rs12828647	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1304496	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1354794	0.89[AMR][1000 genomes]
rs1354795	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1395514	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1466972	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1466973	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1506883	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1506884	0.83[EUR][1000 genomes]
rs1506885	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1506888	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1506890	0.81[EUR][1000 genomes]
rs1580976	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1605329	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1605330	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1605331	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1605333	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1605334	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1605335	0.81[EUR][1000 genomes]
rs17120134	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17120179	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17120182	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1848129	0.84[ASN][1000 genomes]
rs1857941	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1911258	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1911259	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1911260	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1911261	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1911262	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2002580	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2089377	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2102349	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2372376	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2372377	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2372378	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2372379	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2659639	0.80[EUR][1000 genomes]
rs2659659	0.89[ASN][1000 genomes]
rs2659662	0.84[ASN][1000 genomes]
rs2659665	0.80[EUR][1000 genomes]
rs2717404	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720173	0.85[AMR][1000 genomes]
rs2720176	0.84[AMR][1000 genomes]
rs2720178	0.84[AMR][1000 genomes]
rs2720181	0.80[EUR][1000 genomes]
rs2720191	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2888299	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34504532	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34885501	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35195629	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35264128	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35403899	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35599363	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs3858557	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3858558	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3913866	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3933982	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4257013	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4403837	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4435045	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4439558	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4444117	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4465402	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4489786	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4495927	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4565944	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4575322	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4604932	0.83[EUR][1000 genomes]
rs4760181	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760186	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4760187	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4760188	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4760361	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4760362	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4760364	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4760365	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4760366	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6581170	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581171	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6581173	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6581177	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6581178	0.80[AMR][1000 genomes]
rs66832796	0.83[EUR][1000 genomes]
rs7132168	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7132521	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7135063	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7135328	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135728	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7136458	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7139165	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7301724	0.83[EUR][1000 genomes]
rs7304458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304628	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304755	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7308860	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7309322	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7309793	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7309912	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs7314066	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7484670	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7954291	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7954592	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7954914	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7959717	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7959747	0.83[EUR][1000 genomes]
rs7960690	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7960942	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7963367	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970516	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7972562	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7974754	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7975805	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7977671	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7978423	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7979813	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7980024	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7980627	0.83[AMR][1000 genomes]
rs871907	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs871908	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs951901	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs970249	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs982492	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1051716	chr12:58374313-58410810	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2221541	XRCC6BP1	cis	lung	GTEx
rs2221541	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs2221541	XRCC6BP1	cis	Nerve Tibial	GTEx
rs2221541	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs2221541	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs2221541	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs2221541	DKFZP586D0919	cis	multi-tissue	Pritchard
rs2221541	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs2221541	XRCC6BP1	cis	Thyroid	GTEx
rs2221541	XRCC6BP1	cis	multi-tissue	Pritchard
rs2221541	MAP3K12	cis	cerebellum	SCAN
rs2221541	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs2221541	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs2221541	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs2221541	XRCC6BP1	cis	Whole Blood	GTEx
rs2221541	XRCC6BP1	cis	Artery Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58394800-58402800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:58402000-58404000	Enhancers	Brain Germinal Matrix	brain
3	chr12:58402200-58409400	Weak transcription	Esophagus	oesophagus

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