Variant report

Variant	rs2372379
Chromosome Location	chr12:58378795-58378796
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58378763-58378813	HMEC	breast:	n/a
2	chr12:58378763-58378813	NHDF-neo	bronchial:	n/a
3	chr12:58378763-58378813	K562	blood:	n/a
4	chr12:58378763-58378813	MCF10A-Er-Src	breast:	n/a
5	chr12:58378763-58378813	HL-60	blood:	n/a
6	chr12:58378763-58378813	LNCaP	prostate:	n/a
7	chr12:58378763-58378813	PrEC	prostate:	n/a
8	chr12:58378763-58378813	Hepatocyte	liver:	n/a
9	chr12:58378763-58378813	HUVEC	blood vessel:	n/a
10	chr12:58378763-58378813	SK-N-MC	brain:	n/a
11	chr12:58378763-58378813	HNPCEpiC	eye:	n/a
12	chr12:58378763-58378813	Jurkat	blood:	n/a
13	chr12:58378763-58378813	BJ	skin:	n/a
14	chr12:58378763-58378813	HCM	heart:	n/a
15	chr12:58378763-58378813	AG04450	lung:	fetal
16	chr12:58378763-58378813	AG10803	skin:	n/a
17	chr12:58378763-58378813	AoSMC	blood vessel:	n/a
18	chr12:58378763-58378813	HRE	kidney:	n/a
19	chr12:58378763-58378813	GM06990	blood:	n/a
20	chr12:58378763-58378813	GM19239	blood:	n/a
21	chr12:58378763-58378813	NH-A	brain:	n/a
22	chr12:58378763-58378813	AG09319	gingival:	n/a
23	chr12:58378763-58378813	HRPEpiC	eye:	n/a
24	chr12:58378763-58378813	SKMC	muscle:	n/a
25	chr12:58378763-58378813	H1-hESC	embryonic stem cell:	embryo
26	chr12:58378763-58378813	AG09309	skin:	n/a
27	chr12:58378763-58378813	ECC-1	luminal epithelium:	n/a
28	chr12:58378763-58378813	ovcar-3	ovarian:	n/a
29	chr12:58378763-58378813	A549	lung:	n/a
30	chr12:58378763-58378813	SK-N-SH_RA	brain:	n/a
31	chr12:58378763-58378813	HPAEpiC	pulmonary alveolar:	n/a
32	chr12:58378763-58378813	PFSK-1	brain:	n/a
33	chr12:58378763-58378813	Hela-S3	cervix:	n/a
34	chr12:58378763-58378813	HCT-116	colon:	n/a
35	chr12:58378763-58378813	Caco-2	colon:	n/a
36	chr12:58378763-58378813	NHBE	bronchial:	n/a
37	chr12:58378763-58378813	PANC-1	pancreas:	n/a
38	chr12:58378763-58378813	SAEC	small airway:	n/a
39	chr12:58378763-58378813	CMK	blood:	n/a
40	chr12:58378763-58378813	HCPEpiC	choroid plexus:	n/a
41	chr12:58378763-58378813	NT2-D1	testis:	n/a
42	chr12:58378763-58378813	HEEpiC	esophagus:	n/a
43	chr12:58378763-58378813	MCF-7	breast:	n/a
44	chr12:58378763-58378813	HepG2	liver:	n/a
45	chr12:58378763-58378813	BE2_C	brain:	n/a
46	chr12:58378763-58378813	IMR90	lung:	fetal
47	chr12:58378763-58378813	HIPEpiC	eye:	n/a
48	chr12:58378763-58378813	HAEpiC	amniotic membrane:	n/a
49	chr12:58378763-58378813	SK-N-SH	brain:	n/a
50	chr12:58378763-58378813	U87	brain:	n/a

No data

Variant related genes	Relation type
ENSG00000257668	CpG island

Extended variants
information (count: 140 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10431506	0.80[CHD][hapmap]
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]
rs2372378	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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2372379	XRCC6BP1	cis	Nerve Tibial	GTEx
rs2372379	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs2372379	XRCC6BP1	cis	lung	GTEx
rs2372379	XRCC6BP1	cis	Thyroid	GTEx
rs2372379	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs2372379	XRCC6BP1	cis	multi-tissue	Pritchard
rs2372379	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs2372379	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs2372379	XRCC6BP1	cis	Artery Tibial	GTEx
rs2372379	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs2372379	KUB3	cis	multi-tissue	Pritchard
rs2372379	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs2372379	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs2372379	MAP3K12	cis	cerebellum	SCAN
rs2372379	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs2372379	XRCC6BP1	cis	Whole Blood	GTEx

Chromatin state (count:10 , 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	chr12:58377600-58378800	Enhancers	Left Ventricle	heart
3	chr12:58377800-58379200	Weak transcription	Right Atrium	heart
4	chr12:58378000-58383200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:58378000-58393400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:58378400-58378800	Enhancers	Esophagus	oesophagus
7	chr12:58378400-58378800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr12:58378400-58378800	Enhancers	Fetal Muscle Leg	muscle
9	chr12:58378600-58379000	Weak transcription	Adipose Nuclei	Adipose
10	chr12:58378600-58379400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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