Variant report

Variant	rs2372378
Chromosome Location	chr12:58379224-58379225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10506393	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10747790	0.86[AMR][1000 genomes]
rs10783860	0.87[ASN][1000 genomes]
rs10783864	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783865	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10783866	0.86[AMR][1000 genomes]
rs10783867	0.86[AMR][1000 genomes]
rs10783868	0.86[AMR][1000 genomes]
rs10877048	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877050	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10877052	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877053	0.83[AMR][1000 genomes]
rs10877055	0.86[AMR][1000 genomes]
rs10877056	0.86[AMR][1000 genomes]
rs10877066	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10877067	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172408	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172418	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172419	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11172420	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172421	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172422	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172425	0.86[AMR][1000 genomes]
rs11172427	0.86[AMR][1000 genomes]
rs11172446	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11608333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608939	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11615925	0.83[EUR][1000 genomes]
rs11834786	0.86[AMR][1000 genomes]
rs11834807	0.86[AMR][1000 genomes]
rs12366757	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366794	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368024	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12422985	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12580381	0.86[AMR][1000 genomes]
rs12824706	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12825843	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12828647	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1304496	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1354795	0.86[AMR][1000 genomes]
rs1395514	0.86[AMR][1000 genomes]
rs1466972	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1466973	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1506883	0.86[AMR][1000 genomes]
rs1506885	0.86[AMR][1000 genomes]
rs1506888	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1580976	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1605329	0.86[AMR][1000 genomes]
rs1605330	0.86[AMR][1000 genomes]
rs1605331	0.86[AMR][1000 genomes]
rs1605333	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1605334	0.86[AMR][1000 genomes]
rs17120134	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17120179	0.86[AMR][1000 genomes]
rs1848129	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1857941	0.86[AMR][1000 genomes]
rs1911258	0.86[AMR][1000 genomes]
rs1911259	0.86[AMR][1000 genomes]
rs1911260	0.86[AMR][1000 genomes]
rs1911261	0.86[AMR][1000 genomes]
rs1911262	0.83[AMR][1000 genomes]
rs2002580	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2089377	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2102349	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2221541	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2372377	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2372379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659659	0.93[ASN][1000 genomes]
rs2659662	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2717404	0.93[ASN][1000 genomes]
rs2720191	0.93[ASN][1000 genomes]
rs2888299	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34504532	0.86[AMR][1000 genomes]
rs34885501	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35195629	0.86[AMR][1000 genomes]
rs35599363	0.82[AMR][1000 genomes]
rs3858557	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3858558	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3913866	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3933982	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4435045	0.86[AMR][1000 genomes]
rs4444117	0.86[AMR][1000 genomes]
rs4465402	0.86[AMR][1000 genomes]
rs4489786	0.86[AMR][1000 genomes]
rs4495927	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4565944	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4575322	0.86[AMR][1000 genomes]
rs4604932	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4760175	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760181	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760182	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760186	0.86[AMR][1000 genomes]
rs4760361	0.81[AMR][1000 genomes]
rs4760362	0.84[AMR][1000 genomes]
rs4760364	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4760365	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4760366	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6581170	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6581173	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6581177	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7132168	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7132521	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135063	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7135328	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7135728	0.86[AMR][1000 genomes]
rs7136458	0.86[AMR][1000 genomes]
rs7139165	0.86[AMR][1000 genomes]
rs7304458	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7304628	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7304755	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7308860	0.84[AMR][1000 genomes]
rs7309322	0.86[AMR][1000 genomes]
rs7309793	0.83[AMR][1000 genomes]
rs7309912	0.86[AMR][1000 genomes]
rs7314066	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7484670	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7954291	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7954592	0.86[AMR][1000 genomes]
rs7954914	0.83[AMR][1000 genomes]
rs7959717	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7959747	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7960690	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7960942	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7963367	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7970516	0.86[AMR][1000 genomes]
rs7972562	0.83[AMR][1000 genomes]
rs7974754	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7975805	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7977671	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7978423	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7979813	0.85[AMR][1000 genomes]
rs7980024	0.85[AMR][1000 genomes]
rs871907	0.86[AMR][1000 genomes]
rs871908	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs951901	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs970249	0.90[AMR][1000 genomes];0.90[EUR][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	nsv523853	chr12:58350631-58386722	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2372378	XRCC6BP1	cis	Nerve Tibial	GTEx
rs2372378	XRCC6BP1	cis	Artery Tibial	GTEx
rs2372378	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs2372378	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs2372378	XRCC6BP1	cis	lung	GTEx
rs2372378	XRCC6BP1	cis	Thyroid	GTEx
rs2372378	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs2372378	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs2372378	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs2372378	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs2372378	XRCC6BP1	cis	Whole Blood	GTEx
rs2372378	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58377400-58380200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:58378000-58383200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:58378000-58393400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:58378600-58379400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:58379000-58379600	Enhancers	Adipose Nuclei	Adipose
6	chr12:58379200-58379400	Enhancers	Fetal Lung	lung
7	chr12:58379200-58379600	Enhancers	Primary monocytes fromperipheralblood	blood

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