Variant report

Variant	rs3751327
Chromosome Location	chr12:58335274-58335275
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:289)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:289 , 50 per page) page: 1 2 3 4 5 6

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	MXI1	chr12:58334809-58335651	K562	blood:	n/a	n/a
3	MAFK	chr12:58334919-58335460	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:58334782-58335845	Gliobla	brain:	n/a	n/a
5	RELA	chr12:58334859-58335773	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:58334723-58335881	GM15510	blood:	n/a	n/a
7	POLR2A	chr12:58335268-58335660	A549	lung:	n/a	n/a
8	YY1	chr12:58335251-58335744	A549	lung:	n/a	n/a
9	POLR2A	chr12:58334526-58335886	GM19099	blood:	n/a	n/a
10	SIN3AK20	chr12:58334632-58336055	MCF-7	breast:	n/a	n/a
11	POLR2A	chr12:58335267-58335646	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:58334481-58335686	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:58334772-58335666	GM10847	blood:	n/a	n/a
14	TAF1	chr12:58334908-58335289	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr12:58334393-58336278	HL-60	blood:	n/a	n/a
16	TAF1	chr12:58334887-58335693	HepG2	liver:	n/a	n/a
17	TCF12	chr12:58335226-58336024	ECC-1	luminal epithelium:	n/a	chr12:58335747-58335754
18	RCOR1	chr12:58334280-58335545	K562	blood:	n/a	n/a
19	POLR2A	chr12:58334596-58335860	U87	brain:	n/a	n/a
20	GTF2B	chr12:58334871-58335877	K562	blood:	n/a	n/a
21	STAT1	chr12:58334967-58335808	GM12878	blood:	n/a	chr12:58335726-58335738
22	POLR2A	chr12:58334741-58335877	GM18951	blood:	n/a	n/a
23	GABPA	chr12:58334758-58335856	MCF-7	breast:	n/a	n/a
24	TAF1	chr12:58335264-58335784	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZNF384	chr12:58334392-58336970	K562	blood:	n/a	n/a
26	POLR2A	chr12:58334745-58335790	SK-N-MC	brain:	n/a	n/a
27	GATA1	chr12:58333778-58335949	PBDE	blood:	n/a	chr12:58334695-58334704
28	POLR2A	chr12:58334433-58336278	K562	blood:	n/a	n/a
29	MYC	chr12:58334239-58335822	K562	blood:	n/a	chr12:58334323-58334333
30	RELA	chr12:58334527-58336037	GM18951	blood:	n/a	n/a
31	RFX5	chr12:58334732-58335969	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr12:58335264-58335611	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:58334746-58335655	GM12892	blood:	n/a	n/a
34	TBP	chr12:58334841-58336086	Hela-S3	cervix:	n/a	n/a
35	ELF1	chr12:58334606-58335867	MCF-7	breast:	n/a	n/a
36	ARID3A	chr12:58334710-58335423	HepG2	liver:	n/a	n/a
37	TAF7	chr12:58335265-58335750	H1-hESC	embryonic stem cell:	n/a	n/a
38	EP300	chr12:58334905-58335702	T-47D	breast:	n/a	chr12:58335349-58335365 chr12:58334956-58334969
39	TAF1	chr12:58334768-58335508	H1-neurons	neurons:	n/a	n/a
40	ETS1	chr12:58335258-58335747	K562	blood:	n/a	chr12:58335729-58335743
41	POLR2A	chr12:58334037-58336037	PBDE	blood:	n/a	n/a
42	ELF1	chr12:58334678-58335738	MCF-7	breast:	n/a	n/a
43	MTA3	chr12:58334286-58336053	GM12878	blood:	n/a	n/a
44	PML	chr12:58334596-58336147	GM12878	blood:	n/a	n/a
45	POLR2A	chr12:58334655-58335762	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:58334736-58335913	GM18505	blood:	n/a	n/a
47	ZBTB7A	chr12:58334593-58336057	ECC-1	luminal epithelium:	n/a	chr12:58335843-58335852
48	SIN3A	chr12:58334704-58336029	H1-hESC	embryonic stem cell:	n/a	n/a
49	HA-E2F1	chr12:58334745-58335870	MCF-7	breast:	n/a	chr12:58335402-58335414
50	ZMIZ1	chr12:58334526-58335688	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:58334991..58335503-chr19:10764770..10765542,2	NB4	blood:
2	chr12:58334985..58335605-chr13:34391703..34392520,2	NB4	blood:
3	chr12:58238851..58241260-chr12:58332365..58335429,3	K562	blood:
4	chr12:58239271..58242314-chr12:58333147..58337015,4	K562	blood:
5	chr12:58335072..58337363-chr12:62995466..62997804,2	K562	blood:
6	chr12:58176490..58178791-chr12:58333525..58336024,3	K562	blood:
7	chr12:58194367..58196238-chr12:58334648..58336913,2	MCF-7	breast:
8	chr12:58334972..58335922-chr15:44955848..44956364,2	Hela-S3	cervix:
9	chr12:58238634..58240343-chr12:58334223..58336659,2	MCF-7	breast:
10	chr12:58334615..58335529-chr15:72766822..72767478,2	NB4	blood:
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
XRCC6BP1	TF binding region
ENSG00000257921	Chromatin interaction
ENSG00000221949	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000133119	Chromatin interaction
ENSG00000166896	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000129351	Chromatin interaction
ENSG00000199179	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10431506	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10747788	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10783858	0.86[AMR][1000 genomes]
rs10877039	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10877040	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10877041	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11172388	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11172389	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2372309	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3751325	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3751326	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4590915	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4760344	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7358584	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9971803	0.87[AMR][1000 genomes];0.88[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3751327	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs3751327	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs3751327	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs3751327	XRCC6BP1	cis	Artery Aorta	GTEx
rs3751327	XRCC6BP1	cis	Nerve Tibial	GTEx
rs3751327	XRCC6BP1	cis	Thyroid	GTEx
rs3751327	XRCC6BP1	cis	Whole Blood	GTEx
rs3751327	XRCC6BP1	cis	lung	GTEx
rs3751327	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs3751327	XRCC6BP1	cis	Artery Tibial	GTEx
rs3751327	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs3751327	XRCC6BP1	cis	Stomach	GTEx
rs3751327	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs3751327	XRCC6BP1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58334400-58335600	Active TSS	Stomach Smooth Muscle	stomach
2	chr12:58334400-58335800	Active TSS	Brain Cingulate Gyrus	brain
3	chr12:58334400-58335800	Active TSS	Osteobl	bone
4	chr12:58334400-58336000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr12:58334400-58336000	Active TSS	K562	blood
6	chr12:58334400-58336200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr12:58334400-58336200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr12:58334400-58336200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr12:58334600-58335400	Active TSS	Fetal Muscle Trunk	muscle
10	chr12:58334600-58335800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr12:58334600-58335800	Active TSS	HSMMtube	muscle
12	chr12:58334600-58336000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:58334600-58336000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:58334600-58336000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr12:58334600-58336000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:58334600-58336000	Active TSS	Aorta	Aorta
17	chr12:58334600-58336200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr12:58334600-58336200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:58334600-58336200	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr12:58334600-58336200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:58334600-58336200	Active TSS	Fetal Brain Female	brain
22	chr12:58334600-58336200	Active TSS	Fetal Kidney	kidney
23	chr12:58334600-58336200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr12:58334600-58336400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:58334800-58335400	Active TSS	Colonic Mucosa	Colon
26	chr12:58334800-58335400	Weak transcription	Spleen	Spleen
27	chr12:58334800-58335600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:58334800-58335600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:58334800-58335600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:58334800-58335600	Active TSS	Primary T cells from cord blood	blood
31	chr12:58334800-58335600	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr12:58334800-58335600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:58334800-58335600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:58334800-58335600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:58334800-58335600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:58334800-58335600	Active TSS	Liver	Liver
37	chr12:58334800-58335600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr12:58334800-58335600	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr12:58334800-58335600	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr12:58334800-58335600	Active TSS	Rectal Smooth Muscle	rectum
41	chr12:58334800-58335600	Active TSS	Thymus	Thymus
42	chr12:58334800-58335800	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr12:58334800-58335800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:58334800-58335800	Active TSS	Colon Smooth Muscle	Colon
45	chr12:58334800-58335800	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr12:58334800-58335800	Active TSS	Ovary	ovary
47	chr12:58334800-58335800	Active TSS	GM12878-XiMat	blood
48	chr12:58334800-58336000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:58334800-58336000	Active TSS	Esophagus	oesophagus
50	chr12:58334800-58336000	Active TSS	Gastric	stomach

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