Variant report

Variant	rs4760346
Chromosome Location	chr12:58334743-58334744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:128)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:128 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr12:58334538-58336258	K562	blood:	n/a	n/a
2	GABPA	chr12:58334709-58335204	A549	lung:	n/a	n/a
3	POLR2A	chr12:58334723-58335881	GM15510	blood:	n/a	n/a
4	POLR2A	chr12:58334526-58335886	GM19099	blood:	n/a	n/a
5	SIN3AK20	chr12:58334632-58336055	MCF-7	breast:	n/a	n/a
6	POLR2A	chr12:58334481-58335686	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:58334393-58336278	HL-60	blood:	n/a	n/a
8	RCOR1	chr12:58334280-58335545	K562	blood:	n/a	n/a
9	POLR2A	chr12:58334596-58335860	U87	brain:	n/a	n/a
10	POLR2A	chr12:58334741-58335877	GM18951	blood:	n/a	n/a
11	ZNF384	chr12:58334392-58336970	K562	blood:	n/a	n/a
12	BACH1	chr12:58334510-58335059	K562	blood:	n/a	n/a
13	GATA1	chr12:58333778-58335949	PBDE	blood:	n/a	chr12:58334695-58334704
14	POLR2A	chr12:58334433-58336278	K562	blood:	n/a	n/a
15	MYC	chr12:58334239-58335822	K562	blood:	n/a	chr12:58334323-58334333
16	RELA	chr12:58334527-58336037	GM18951	blood:	n/a	n/a
17	RFX5	chr12:58334732-58335969	Hela-S3	cervix:	n/a	n/a
18	ZC3H11A	chr12:58334626-58335194	K562	blood:	n/a	n/a
19	ELF1	chr12:58334606-58335867	MCF-7	breast:	n/a	n/a
20	ARID3A	chr12:58334710-58335423	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:58334037-58336037	PBDE	blood:	n/a	n/a
22	ELF1	chr12:58334678-58335738	MCF-7	breast:	n/a	n/a
23	MTA3	chr12:58334286-58336053	GM12878	blood:	n/a	n/a
24	PML	chr12:58334596-58336147	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:58334655-58335762	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:58334736-58335913	GM18505	blood:	n/a	n/a
27	ZBTB7A	chr12:58334593-58336057	ECC-1	luminal epithelium:	n/a	chr12:58335843-58335852
28	SIN3A	chr12:58334704-58336029	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZMIZ1	chr12:58334526-58335688	K562	blood:	n/a	n/a
30	TCF12	chr12:58334643-58335967	ECC-1	luminal epithelium:	n/a	chr12:58335747-58335754 chr12:58335128-58335138
31	MAX	chr12:58334527-58335916	K562	blood:	n/a	n/a
32	RCOR1	chr12:58334686-58336023	Hela-S3	cervix:	n/a	n/a
33	CUX1	chr12:58333856-58335137	K562	blood:	n/a	n/a
34	EGR1	chr12:58334615-58335172	K562	blood:	n/a	chr12:58334959-58334973
35	RELA	chr12:58334711-58335884	GM19099	blood:	n/a	n/a
36	POLR2A	chr12:58334742-58335877	GM19193	blood:	n/a	n/a
37	HEY1	chr12:58334519-58335227	K562	blood:	n/a	n/a
38	POLR2A	chr12:58334516-58336259	K562	blood:	n/a	n/a
39	TAF1	chr12:58334726-58335923	ECC-1	luminal epithelium:	n/a	n/a
40	JUN	chr12:58334422-58335751	K562	blood:	n/a	n/a
41	UBTF	chr12:58334572-58335793	K562	blood:	n/a	n/a
42	ARID3A	chr12:58334350-58335115	K562	blood:	n/a	chr12:58334549-58334565
43	MAZ	chr12:58334556-58335933	Hela-S3	cervix:	n/a	n/a
44	MYC	chr12:58334184-58336205	K562	blood:	n/a	chr12:58334323-58334333
45	PML	chr12:58334403-58336190	K562	blood:	n/a	n/a
46	MAX	chr12:58334645-58335933	A549	lung:	n/a	n/a
47	KAP1	chr12:58334466-58335152	HEK293	kidney:	n/a	n/a
48	POLR2A	chr12:58334520-58336270	K562	blood:	n/a	n/a
49	MXI1	chr12:58334616-58335917	IMR90	lung:	n/a	n/a
50	ELK1	chr12:58334571-58335167	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58160622..58162536-chr12:58333544..58335201,2	K562	blood:
2	chr12:58238851..58241260-chr12:58332365..58335429,3	K562	blood:
3	chr12:58239271..58242314-chr12:58333147..58337015,4	K562	blood:
4	chr12:42719596..42720261-chr12:58334471..58335198,2	Hela-S3	cervix:
5	chr12:58176490..58178791-chr12:58333525..58336024,3	K562	blood:
6	chr12:58194367..58196238-chr12:58334648..58336913,2	MCF-7	breast:
7	chr12:58327474..58329106-chr12:58333139..58335115,2	MCF-7	breast:
8	chr12:58238634..58240343-chr12:58334223..58336659,2	MCF-7	breast:
9	chr12:58334615..58335529-chr15:72766822..72767478,2	NB4	blood:
10	chr12:58162992..58165092-chr12:58332637..58335110,2	MCF-7	breast:
11	chr12:58334540..58337378-chr12:58339251..58345306,6	MCF-7	breast:
12	chr12:58164836..58167188-chr12:58333922..58337646,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257698	TF binding region
XRCC6BP1	TF binding region
ENSG00000139168	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000134283	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000166896	Chromatin interaction
ENSG00000135407	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10122	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10431506	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs10747788	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs10783859	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877036	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877037	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877040	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs10877041	0.80[EUR][1000 genomes]
rs11172387	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172388	0.80[EUR][1000 genomes]
rs12308413	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2372309	0.80[EUR][1000 genomes]
rs2888288	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751325	0.80[EUR][1000 genomes]
rs3751326	0.80[EUR][1000 genomes]
rs4237845	0.80[JPT][hapmap]
rs4272820	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4335583	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4373979	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4509811	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4534624	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4583019	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760174	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760343	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760344	0.80[EUR][1000 genomes]
rs4760347	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6581159	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7133278	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136981	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7295748	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7298370	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7299249	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7358584	0.80[EUR][1000 genomes]
rs7954957	0.80[JPT][hapmap]
rs7975227	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7978588	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9971722	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4760346	XRCC6BP1	cis	Whole Blood	GTEx
rs4760346	XRCC6BP1	cis	Thyroid	GTEx
rs4760346	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs4760346	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs4760346	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs4760346	XRCC6BP1	cis	lung	GTEx
rs4760346	XRCC6BP1	cis	Artery Tibial	GTEx
rs4760346	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs4760346	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs4760346	SMARCC2	cis	cerebellum	SCAN
rs4760346	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs4760346	IL23A	cis	cerebellum	SCAN
rs4760346	XRCC6BP1	cis	Nerve Tibial	GTEx
rs4760346	KIAA0748	cis	cerebellum	SCAN
rs4760346	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4760346	XRCC6BP1	cis	Artery Aorta	GTEx
rs4760346	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760346	FAM119B	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58330200-58334800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:58334200-58334800	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr12:58334200-58335000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr12:58334200-58335000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
5	chr12:58334200-58335000	Flanking Active TSS	Dnd41	blood
6	chr12:58334200-58335000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr12:58334200-58335200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr12:58334400-58334800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:58334400-58334800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr12:58334400-58334800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr12:58334400-58334800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:58334400-58334800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:58334400-58334800	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr12:58334400-58334800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr12:58334400-58334800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:58334400-58334800	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr12:58334400-58334800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:58334400-58334800	Flanking Active TSS	Colonic Mucosa	Colon
19	chr12:58334400-58334800	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr12:58334400-58334800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr12:58334400-58334800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr12:58334400-58334800	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr12:58334400-58334800	Enhancers	Small Intestine	intestine
24	chr12:58334400-58334800	Flanking Active TSS	Thymus	Thymus
25	chr12:58334400-58334800	Flanking Active TSS	GM12878-XiMat	blood
26	chr12:58334400-58335000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
27	chr12:58334400-58335000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:58334400-58335000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:58334400-58335000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:58334400-58335000	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr12:58334400-58335000	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr12:58334400-58335000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr12:58334400-58335000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr12:58334400-58335000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:58334400-58335000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:58334400-58335000	Flanking Active TSS	Hela-S3	cervix
37	chr12:58334400-58335000	Flanking Active TSS	HepG2	liver
38	chr12:58334400-58335000	Flanking Active TSS	NHDF-Ad	bronchial
39	chr12:58334400-58335200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr12:58334400-58335200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:58334400-58335600	Active TSS	Stomach Smooth Muscle	stomach
42	chr12:58334400-58335800	Active TSS	Brain Cingulate Gyrus	brain
43	chr12:58334400-58335800	Active TSS	Osteobl	bone
44	chr12:58334400-58336000	Active TSS	H9 Cell Line	embryonic stem cell
45	chr12:58334400-58336000	Active TSS	K562	blood
46	chr12:58334400-58336200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr12:58334400-58336200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr12:58334400-58336200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr12:58334600-58334800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:58334600-58334800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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