Variant report

Variant	rs3751331
Chromosome Location	chr12:58290278-58290279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58288646-58291559	SK-N-MC	brain:	n/a	n/a
2	MAX	chr12:58290226-58291007	H1-hESC	embryonic stem cell:	n/a	chr12:58290564-58290577
3	EP300	chr12:58290080-58290932	ECC-1	luminal epithelium:	n/a	n/a
4	TAF1	chr12:58290221-58291048	ECC-1	luminal epithelium:	n/a	n/a
5	E2F6	chr12:58290227-58291052	H1-hESC	embryonic stem cell:	n/a	chr12:58290359-58290369 chr12:58290572-58290586 chr12:58290576-58290583 chr12:58290358-58290367 chr12:58290449-58290458 chr12:58290576-58290583 chr12:58290576-58290583
6	PBX3	chr12:58290274-58290895	SK-N-SH	brain:	n/a	n/a
7	MAX	chr12:58290170-58291177	ECC-1	luminal epithelium:	n/a	chr12:58290564-58290577
8	ELF1	chr12:58290004-58290597	GM12878	blood:	n/a	chr12:58290361-58290370 chr12:58290353-58290365
9	POLR2A	chr12:58290272-58290580	A549	lung:	n/a	n/a
10	POLR2A	chr12:58289450-58291018	U87	brain:	n/a	n/a
11	POLR2A	chr12:58290239-58290682	HUVEC	blood vessel:	n/a	n/a
12	MAX	chr12:58290235-58291055	A549	lung:	n/a	chr12:58290564-58290577
13	ZNF263	chr12:58290066-58291702	HEK293-T-REx	kidney:	n/a	chr12:58290542-58290551 chr12:58291423-58291444
14	ZBTB7A	chr12:58289919-58291121	ECC-1	luminal epithelium:	n/a	n/a
15	CTCF	chr12:58290260-58290410	NHDF-neo	bronchial:	n/a	n/a
16	USF1	chr12:58290145-58290881	SK-N-SH	brain:	n/a	chr12:58290352-58290368 chr12:58290360-58290376 chr12:58290309-58290325
17	SMC3	chr12:58289586-58291477	SK-N-SH	brain:	n/a	chr12:58291369-58291379
18	TCF12	chr12:58289963-58291194	A549	lung:	n/a	n/a
19	MAX	chr12:58290168-58291087	ECC-1	luminal epithelium:	n/a	chr12:58290564-58290577
20	EP300	chr12:58290192-58290926	SK-N-SH	brain:	n/a	n/a
21	SP1	chr12:58290198-58291102	A549	lung:	n/a	chr12:58290696-58290706 chr12:58290540-58290554 chr12:58290531-58290545 chr12:58290753-58290767
22	TCF12	chr12:58290051-58290913	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr12:58290131-58291153	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr12:58290253-58291417	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr12:58289916-58291130	SK-N-SH	brain:	n/a	n/a
26	MAX	chr12:58290272-58290684	H1-hESC	embryonic stem cell:	n/a	chr12:58290564-58290577
27	MAX	chr12:58290083-58291190	A549	lung:	n/a	chr12:58290564-58290577
28	E2F6	chr12:58290242-58290859	A549	lung:	n/a	chr12:58290359-58290369 chr12:58290572-58290586 chr12:58290576-58290583 chr12:58290358-58290367 chr12:58290449-58290458 chr12:58290576-58290583 chr12:58290576-58290583
29	RAD21	chr12:58289720-58291548	SK-N-SH	brain:	n/a	chr12:58290718-58290728 chr12:58291323-58291335 chr12:58291514-58291528
30	POLR2A	chr12:58290088-58291015	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr12:58290140-58290290	HCM	heart:	n/a	n/a
32	MAX	chr12:58290260-58291088	SK-N-SH	brain:	n/a	chr12:58290564-58290577
33	POLR2A	chr12:58290164-58290983	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr12:58290273-58290295	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr12:58290234-58291099	HUVEC	blood vessel:	n/a	n/a
36	USF1	chr12:58290222-58291082	ECC-1	luminal epithelium:	n/a	chr12:58290352-58290368 chr12:58290360-58290376 chr12:58290309-58290325
37	POLR2A	chr12:58289793-58290780	SK-N-MC	brain:	n/a	n/a
38	MAZ	chr12:58289185-58291043	IMR90	lung:	n/a	chr12:58290564-58290577
39	ZBTB7A	chr12:58289872-58291151	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr12:58289841-58290703	U87	brain:	n/a	n/a
41	POLR2A	chr12:58290195-58290743	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr12:58290239-58290623	A549	lung:	n/a	n/a
43	POLR2A	chr12:58290212-58290547	A549	lung:	n/a	n/a
44	POLR2A	chr12:58290202-58290497	ProgFib	skin:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58290233-58290283	ProgFib	skin:	n/a
2	chr12:58290233-58290283	HUVEC	blood vessel:	n/a
3	chr12:58290233-58290283	PANC-1	pancreas:	n/a
4	chr12:58290233-58290283	AG04450	lung:	fetal
5	chr12:58290233-58290283	NH-A	brain:	n/a
6	chr12:58290233-58290283	HNPCEpiC	eye:	n/a
7	chr12:58290233-58290283	HEEpiC	esophagus:	n/a
8	chr12:58290233-58290283	T-47D	breast:	n/a
9	chr12:58290233-58290283	HRE	kidney:	n/a
10	chr12:58290233-58290283	A549	lung:	n/a
11	chr12:58290233-58290283	SK-N-SH	brain:	n/a
12	chr12:58290233-58290283	GM19239	blood:	n/a
13	chr12:58290233-58290283	SK-N-SH_RA	brain:	n/a
14	chr12:58290233-58290283	AoSMC	blood vessel:	n/a
15	chr12:58290233-58290283	ECC-1	luminal epithelium:	n/a
16	chr12:58290233-58290283	AG04449	skin:	fetal
17	chr12:58290233-58290283	HCPEpiC	choroid plexus:	n/a
18	chr12:58290233-58290283	NT2-D1	testis:	n/a
19	chr12:58290233-58290283	BJ	skin:	n/a
20	chr12:58290233-58290283	ovcar-3	ovarian:	n/a
21	chr12:58290233-58290283	Hela-S3	cervix:	n/a
22	chr12:58290233-58290283	HL-60	blood:	n/a
23	chr12:58290233-58290283	BE2_C	brain:	n/a
24	chr12:58290233-58290283	NHBE	bronchial:	n/a
25	chr12:58290233-58290283	HRCEpiC	kidney:	n/a
26	chr12:58290233-58290283	HCM	heart:	n/a
27	chr12:58290233-58290283	U87	brain:	n/a
28	chr12:58290233-58290283	HCF	heart:	n/a
29	chr12:58290233-58290283	HCT-116	colon:	n/a
30	chr12:58290233-58290283	HMEC	breast:	n/a
31	chr12:58290233-58290283	GM06990	blood:	n/a
32	chr12:58290233-58290283	AG10803	skin:	n/a
33	chr12:58290233-58290283	HIPEpiC	eye:	n/a
34	chr12:58290233-58290283	LNCaP	prostate:	n/a
35	chr12:58290233-58290283	HepG2	liver:	n/a
36	chr12:58290233-58290283	NB4	blood:	n/a
37	chr12:58290233-58290283	MCF-7	breast:	n/a
38	chr12:58290233-58290283	MCF10A-Er-Src	breast:	n/a
39	chr12:58290233-58290283	Caco-2	colon:	n/a
40	chr12:58290233-58290283	SAEC	small airway:	n/a
41	chr12:58290233-58290283	GM12892	blood:	n/a
42	chr12:58290233-58290283	GM12878	blood:	n/a
43	chr12:58290233-58290283	HEK293	kidney:	embryo
44	chr12:58290233-58290283	AG09319	gingival:	n/a
45	chr12:58290233-58290283	PrEC	prostate:	n/a
46	chr12:58290233-58290283	RPTEC	kidney:	n/a
47	chr12:58290233-58290283	Jurkat	blood:	n/a
48	chr12:58290233-58290283	HAEpiC	amniotic membrane:	n/a
49	chr12:58290233-58290283	IMR90	lung:	fetal
50	chr12:58290233-58290283	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58238802..58241111-chr12:58289482..58291156,2	K562	blood:
2	chr12:58236711..58242486-chr12:58286970..58293951,15	MCF-7	breast:
3	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:
4	chr12:58166094..58167924-chr12:58290124..58292095,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XRCC6BP1-1	chr12:58289435-58290670	XLOC_009779

Variant related genes	Relation type
ENSG00000245651	TF binding region
ENSG00000245651	CpG island
ENSG00000175215	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000037897	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10444569	0.83[ASN][1000 genomes]
rs10747786	0.80[ASN][1000 genomes]
rs10747787	0.80[ASN][1000 genomes]
rs10877031	0.83[ASN][1000 genomes]
rs10877032	0.83[ASN][1000 genomes]
rs10877033	0.82[ASN][1000 genomes]
rs10877034	0.80[ASN][1000 genomes]
rs11172367	0.83[ASN][1000 genomes]
rs11172368	0.83[ASN][1000 genomes]
rs11172369	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11172371	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11172372	0.82[ASN][1000 genomes]
rs11172375	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172378	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12319233	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12426201	0.83[ASN][1000 genomes]
rs1599931	0.83[ASN][1000 genomes]
rs1962047	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002275	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3751330	0.83[ASN][1000 genomes]
rs4128707	0.83[ASN][1000 genomes]
rs4237844	0.83[ASN][1000 genomes]
rs4237845	0.80[ASN][1000 genomes]
rs4628718	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4630335	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760339	0.83[ASN][1000 genomes]
rs4760341	0.82[ASN][1000 genomes]
rs59401446	0.80[ASN][1000 genomes]
rs61935769	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6650217	0.83[ASN][1000 genomes]
rs6650218	0.83[ASN][1000 genomes]
rs6650219	0.83[ASN][1000 genomes]
rs7134797	0.81[ASN][1000 genomes]
rs7306124	0.83[EUR][1000 genomes]
rs7312623	0.83[ASN][1000 genomes]
rs7954591	0.83[ASN][1000 genomes]
rs7954957	0.83[ASN][1000 genomes]
rs7963992	0.82[ASN][1000 genomes]
rs7969844	0.81[ASN][1000 genomes]
rs7971877	0.80[ASN][1000 genomes]
rs9645819	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3751331	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs3751331	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs3751331	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs3751331	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs3751331	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs3751331	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs3751331	XRCC6BP1	cis	Thyroid	GTEx
rs3751331	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs3751331	XRCC6BP1	cis	Artery Tibial	GTEx
rs3751331	XRCC6BP1	cis	Nerve Tibial	GTEx
rs3751331	XRCC6BP1	cis	Artery Aorta	GTEx
rs3751331	XRCC6BP1	cis	Whole Blood	GTEx
rs3751331	XRCC6BP1	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58286000-58290600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:58286800-58291400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:58287800-58290400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:58287800-58290400	Flanking Active TSS	NHDF-Ad	bronchial
5	chr12:58288200-58293200	Enhancers	Spleen	Spleen
6	chr12:58288400-58290600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr12:58288400-58291000	Weak transcription	K562	blood
8	chr12:58288400-58292000	Weak transcription	Hela-S3	cervix
9	chr12:58289000-58290400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:58289200-58290400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:58289200-58290400	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr12:58289200-58290400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr12:58289200-58290400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr12:58289200-58293400	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr12:58289400-58291400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:58289600-58290400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr12:58289600-58290400	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr12:58289600-58290400	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr12:58289600-58290400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr12:58289600-58290400	Flanking Active TSS	Osteobl	bone
21	chr12:58289600-58291200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr12:58289600-58291200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr12:58289600-58291200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:58289600-58291400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:58289800-58290400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:58289800-58290400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr12:58289800-58290400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:58289800-58290400	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr12:58289800-58290400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr12:58289800-58290400	Flanking Active TSS	A549	lung
31	chr12:58289800-58290800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:58289800-58291000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr12:58289800-58291000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr12:58289800-58291000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:58289800-58291000	Active TSS	Aorta	Aorta
36	chr12:58289800-58291200	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr12:58289800-58291200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:58289800-58291200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
39	chr12:58289800-58291400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:58290000-58290400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:58290000-58290400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:58290000-58290400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
43	chr12:58290000-58290400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:58290000-58290400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:58290000-58290400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
46	chr12:58290000-58290400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
47	chr12:58290000-58290400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:58290000-58290400	Flanking Active TSS	Colonic Mucosa	Colon
49	chr12:58290000-58290400	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr12:58290000-58290400	Flanking Active TSS	Placenta	Placenta

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