Variant report

Variant	rs1580976
Chromosome Location	chr12:58461697-58461698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58460244..58462054-chr12:58476123..58478846,2	MCF-7	breast:
2	chr12:58461282..58462971-chr12:58479054..58481016,2	MCF-7	breast:
3	chr12:58336020..58338569-chr12:58461127..58463440,2	MCF-7	breast:
4	chr12:58460641..58463046-chr12:58464806..58468044,3	MCF-7	breast:

Extended variants
information (count: 166 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs1027800	0.90[ASN][1000 genomes]
rs10506393	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10747790	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10783865	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783866	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10783867	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10783868	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10783873	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877048	0.83[EUR][1000 genomes]
rs10877050	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10877052	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10877053	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10877055	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10877056	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10877065	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877066	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877067	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877069	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11172408	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11172418	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11172419	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11172420	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11172421	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11172422	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11172425	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11172427	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11172446	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172456	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172457	0.83[EUR][1000 genomes]
rs11608333	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11608939	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11615925	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11615944	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11615959	0.80[AMR][1000 genomes]
rs11834786	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11834807	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12366757	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12366794	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12368024	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12422985	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12580381	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12820787	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12824706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12828647	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1304496	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1354794	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1354795	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1395511	0.90[ASN][1000 genomes]
rs1395514	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1466972	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1466973	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1506883	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1506884	0.80[EUR][1000 genomes]
rs1506885	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1506888	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1506890	0.91[ASN][1000 genomes]
rs1567130	0.90[ASN][1000 genomes]
rs1580977	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1605329	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1605330	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1605331	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1605333	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1605334	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1605335	0.91[ASN][1000 genomes]
rs17120134	0.83[AMR][1000 genomes]
rs17120179	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17120182	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1857941	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1911258	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1911259	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1911260	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1911261	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1911262	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1995655	0.82[ASN][1000 genomes]
rs2002580	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2089377	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2102349	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2221541	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2372376	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2372377	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2372378	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2372379	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2659639	0.91[ASN][1000 genomes]
rs2659641	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659646	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659665	0.91[ASN][1000 genomes]
rs2720173	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2720176	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2720178	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720179	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2720181	0.88[ASN][1000 genomes]
rs2888299	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34504532	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34885501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35195629	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35264128	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35599363	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs36174144	0.85[ASN][1000 genomes]
rs3858557	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3858558	0.84[EUR][1000 genomes]
rs3933982	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4257013	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4403837	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4435045	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4444117	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4465402	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4489786	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4495927	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4565944	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4575322	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4760181	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4760182	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4760186	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4760187	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4760188	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760361	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760362	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4760364	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760366	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581170	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6581173	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6581177	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7132168	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7132521	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7135063	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7135328	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7135728	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7136458	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7139165	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs71461350	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7304458	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7304628	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7304755	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7308860	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7309322	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7309793	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7309912	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7314066	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7484670	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7954592	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7954914	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7959717	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7960690	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7960942	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7963367	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7970516	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7972562	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7974754	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7975711	0.84[ASN][1000 genomes]
rs7975805	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7976016	0.84[ASN][1000 genomes]
rs7978423	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7979813	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7980024	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7980627	0.90[ASN][1000 genomes]
rs871907	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs871908	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs951901	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs970249	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs982492	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs982493	0.81[EUR][1000 genomes];0.98[ASN][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	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
3	esv3502230	chr12:58458209-58490226	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3502241	chr12:58458223-58490223	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1580976	XRCC6BP1	cis	Nerve Tibial	GTEx
rs1580976	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs1580976	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs1580976	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs1580976	XRCC6BP1	cis	Thyroid	GTEx
rs1580976	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs1580976	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs1580976	XRCC6BP1	cis	lung	GTEx
rs1580976	XRCC6BP1	cis	Whole Blood	GTEx
rs1580976	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs1580976	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs1580976	XRCC6BP1	cis	Artery Tibial	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58459000-58464400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:58459400-58461800	Enhancers	HMEC	breast
3	chr12:58459400-58464600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:58459800-58464400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:58459800-58464400	Enhancers	Hela-S3	cervix
6	chr12:58459800-58464400	Enhancers	NHEK	skin
7	chr12:58460200-58463000	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:58461200-58462000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:58461200-58462000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:58461200-58462000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:58461200-58462000	Enhancers	Pancreas	Pancrea
12	chr12:58461200-58462000	Enhancers	NH-A	brain
13	chr12:58461200-58462200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:58461200-58462200	Enhancers	Esophagus	oesophagus
15	chr12:58461600-58462200	Enhancers	Fetal Kidney	kidney

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