Variant report

Variant	rs4590915
Chromosome Location	chr12:58335130-58335131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:306)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:306 , 50 per page) page: 1 2 3 4 5 6 7

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	YY1	chr12:58334761-58335199	SK-N-SH_RA	brain:	n/a	chr12:58334851-58334867 chr12:58335146-58335157
5	TAF1	chr12:58334842-58335178	GM12891	blood:	n/a	n/a
6	SIN3AK20	chr12:58334812-58335235	K562	blood:	n/a	n/a
7	POLR2A	chr12:58334782-58335845	Gliobla	brain:	n/a	n/a
8	RELA	chr12:58334859-58335773	GM12892	blood:	n/a	n/a
9	GABPA	chr12:58334709-58335204	A549	lung:	n/a	n/a
10	POLR2A	chr12:58334723-58335881	GM15510	blood:	n/a	n/a
11	TAF1	chr12:58334968-58335226	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:58334526-58335886	GM19099	blood:	n/a	n/a
13	SIN3AK20	chr12:58334632-58336055	MCF-7	breast:	n/a	n/a
14	POLR2A	chr12:58334481-58335686	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:58334772-58335666	GM10847	blood:	n/a	n/a
16	ZNF143	chr12:58334773-58335139	K562	blood:	n/a	n/a
17	TAF1	chr12:58334908-58335289	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr12:58334393-58336278	HL-60	blood:	n/a	n/a
19	TAF1	chr12:58334887-58335693	HepG2	liver:	n/a	n/a
20	RCOR1	chr12:58334280-58335545	K562	blood:	n/a	n/a
21	POLR2A	chr12:58334596-58335860	U87	brain:	n/a	n/a
22	GTF2B	chr12:58334871-58335877	K562	blood:	n/a	n/a
23	STAT1	chr12:58334967-58335808	GM12878	blood:	n/a	chr12:58335726-58335738
24	EGR1	chr12:58334842-58335170	GM12878	blood:	n/a	chr12:58334959-58334973
25	POLR2A	chr12:58334741-58335877	GM18951	blood:	n/a	n/a
26	SIN3AK20	chr12:58334990-58335239	HepG2	liver:	n/a	n/a
27	GABPA	chr12:58334758-58335856	MCF-7	breast:	n/a	n/a
28	ZNF384	chr12:58334392-58336970	K562	blood:	n/a	n/a
29	POLR2A	chr12:58334745-58335790	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr12:58334787-58335224	PANC-1	pancreas:	n/a	n/a
31	GATA1	chr12:58333778-58335949	PBDE	blood:	n/a	chr12:58334695-58334704
32	POLR2A	chr12:58334433-58336278	K562	blood:	n/a	n/a
33	MYC	chr12:58334239-58335822	K562	blood:	n/a	chr12:58334323-58334333
34	RELA	chr12:58334527-58336037	GM18951	blood:	n/a	n/a
35	RFX5	chr12:58334732-58335969	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr12:58334779-58335227	GM12878	blood:	n/a	n/a
37	ZC3H11A	chr12:58334626-58335194	K562	blood:	n/a	n/a
38	POLR2A	chr12:58334746-58335655	GM12892	blood:	n/a	n/a
39	TBP	chr12:58334841-58336086	Hela-S3	cervix:	n/a	n/a
40	ELF1	chr12:58334606-58335867	MCF-7	breast:	n/a	n/a
41	ARID3A	chr12:58334710-58335423	HepG2	liver:	n/a	n/a
42	EP300	chr12:58334905-58335702	T-47D	breast:	n/a	chr12:58335349-58335365 chr12:58334956-58334969
43	POU2F2	chr12:58334966-58335191	GM12878	blood:	n/a	n/a
44	TAF1	chr12:58334768-58335508	H1-neurons	neurons:	n/a	n/a
45	FOXP2	chr12:58334974-58335215	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr12:58334944-58335211	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:58334037-58336037	PBDE	blood:	n/a	n/a
48	ELF1	chr12:58334678-58335738	MCF-7	breast:	n/a	n/a
49	MTA3	chr12:58334286-58336053	GM12878	blood:	n/a	n/a
50	PML	chr12:58334596-58336147	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58334991..58335503-chr19:10764770..10765542,2	NB4	blood:
2	chr12:58160622..58162536-chr12:58333544..58335201,2	K562	blood:
3	chr12:58334985..58335605-chr13:34391703..34392520,2	NB4	blood:
4	chr12:58238851..58241260-chr12:58332365..58335429,3	K562	blood:
5	chr12:58239271..58242314-chr12:58333147..58337015,4	K562	blood:
6	chr12:58335072..58337363-chr12:62995466..62997804,2	K562	blood:
7	chr12:42719596..42720261-chr12:58334471..58335198,2	Hela-S3	cervix:
8	chr12:58176490..58178791-chr12:58333525..58336024,3	K562	blood:
9	chr12:58194367..58196238-chr12:58334648..58336913,2	MCF-7	breast:
10	chr12:58334972..58335922-chr15:44955848..44956364,2	Hela-S3	cervix:
11	chr12:58238634..58240343-chr12:58334223..58336659,2	MCF-7	breast:
12	chr12:58334615..58335529-chr15:72766822..72767478,2	NB4	blood:
13	chr12:58334540..58337378-chr12:58339251..58345306,6	MCF-7	breast:
14	chr12:58164836..58167188-chr12:58333922..58337646,3	K562	blood:

No data

Variant related genes	Relation type
XRCC6BP1	TF binding region
ENSG00000175215	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000134283	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000133119	Chromatin interaction
ENSG00000199179	Chromatin interaction
ENSG00000139168	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000166896	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000221949	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000129351	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10431506	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747788	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783857	0.87[AMR][1000 genomes]
rs10783858	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877039	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877040	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877041	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172388	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172389	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2372309	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751325	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751326	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3751327	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4760344	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7358584	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9971803	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4590915	XRCC6BP1	cis	Stomach	GTEx
rs4590915	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs4590915	XRCC6BP1	cis	Whole Blood	GTEx
rs4590915	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4590915	XRCC6BP1	cis	lung	GTEx
rs4590915	XRCC6BP1	cis	Nerve Tibial	GTEx
rs4590915	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs4590915	ENSG00000166896	cis	multi-tissue	Pritchard
rs4590915	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs4590915	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs4590915	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4590915	XRCC6BP1	cis	Artery Tibial	GTEx
rs4590915	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs4590915	XRCC6BP1	cis	Thyroid	GTEx
rs4590915	XRCC6BP1	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58334200-58335200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr12:58334400-58335200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr12:58334400-58335200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:58334400-58335600	Active TSS	Stomach Smooth Muscle	stomach
5	chr12:58334400-58335800	Active TSS	Brain Cingulate Gyrus	brain
6	chr12:58334400-58335800	Active TSS	Osteobl	bone
7	chr12:58334400-58336000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr12:58334400-58336000	Active TSS	K562	blood
9	chr12:58334400-58336200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr12:58334400-58336200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:58334400-58336200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr12:58334600-58335200	Flanking Active TSS	Fetal Thymus	thymus
13	chr12:58334600-58335400	Active TSS	Fetal Muscle Trunk	muscle
14	chr12:58334600-58335800	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr12:58334600-58335800	Active TSS	HSMMtube	muscle
16	chr12:58334600-58336000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:58334600-58336000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:58334600-58336000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr12:58334600-58336000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:58334600-58336000	Active TSS	Aorta	Aorta
21	chr12:58334600-58336200	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr12:58334600-58336200	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr12:58334600-58336200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr12:58334600-58336200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:58334600-58336200	Active TSS	Fetal Brain Female	brain
26	chr12:58334600-58336200	Active TSS	Fetal Kidney	kidney
27	chr12:58334600-58336200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr12:58334600-58336400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:58334800-58335200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
30	chr12:58334800-58335400	Active TSS	Colonic Mucosa	Colon
31	chr12:58334800-58335400	Weak transcription	Spleen	Spleen
32	chr12:58334800-58335600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:58334800-58335600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:58334800-58335600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:58334800-58335600	Active TSS	Primary T cells from cord blood	blood
36	chr12:58334800-58335600	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr12:58334800-58335600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:58334800-58335600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:58334800-58335600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:58334800-58335600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:58334800-58335600	Active TSS	Liver	Liver
42	chr12:58334800-58335600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr12:58334800-58335600	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr12:58334800-58335600	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr12:58334800-58335600	Active TSS	Rectal Smooth Muscle	rectum
46	chr12:58334800-58335600	Active TSS	Thymus	Thymus
47	chr12:58334800-58335800	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr12:58334800-58335800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:58334800-58335800	Active TSS	Colon Smooth Muscle	Colon
50	chr12:58334800-58335800	Active TSS	Duodenum Smooth Muscle	Duodenum

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