Variant report

Variant	rs3751325
Chromosome Location	chr12:58335626-58335627
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58335319..58338203-chr12:58340129..58346317,10	K562	blood:
2	chr12:58239271..58242314-chr12:58333147..58337015,4	K562	blood:
3	chr12:58335072..58337363-chr12:62995466..62997804,2	K562	blood:
4	chr12:58176490..58178791-chr12:58333525..58336024,3	K562	blood:
5	chr12:58194367..58196238-chr12:58334648..58336913,2	MCF-7	breast:
6	chr12:58334972..58335922-chr15:44955848..44956364,2	Hela-S3	cervix:
7	chr12:58238634..58240343-chr12:58334223..58336659,2	MCF-7	breast:
8	chr12:58334540..58337378-chr12:58339251..58345306,6	MCF-7	breast:
9	chr12:58164836..58167188-chr12:58333922..58337646,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000123427	Chromatin interaction
ENSG00000166896	Chromatin interaction
ENSG00000199179	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000221949	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10431506	0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747788	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783857	0.85[AMR][1000 genomes]
rs10783858	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877039	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877040	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877041	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172387	0.81[EUR][1000 genomes]
rs11172388	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172389	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2372309	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751326	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3751327	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4373979	0.81[EUR][1000 genomes]
rs4509811	0.81[EUR][1000 genomes]
rs4534624	0.81[EUR][1000 genomes]
rs4590915	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760174	0.81[EUR][1000 genomes]
rs4760344	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760346	0.80[EUR][1000 genomes]
rs6581159	0.83[CEU][hapmap]
rs7136981	0.81[EUR][1000 genomes]
rs7298370	0.81[EUR][1000 genomes]
rs7358584	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9971803	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs3751325	XRCC6BP1	cis	lesional skin	skin_eQTL
rs3751325	KUB3	cis	multi-tissue	Pritchard
rs3751325	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs3751325	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs3751325	XRCC6BP1	cis	Artery Tibial	GTEx
rs3751325	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs3751325	XRCC6BP1	cis	Nerve Tibial	GTEx
rs3751325	XRCC6BP1	cis	Artery Aorta	GTEx
rs3751325	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs3751325	XRCC6BP1	cis	normal skin	skin_eQTL
rs3751325	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs3751325	XRCC6BP1	cis	uninvolved skin	skin_eQTL
rs3751325	XRCC6BP1	cis	Lymphoblastoid	GTEx
rs3751325	XRCC6BP1	cis	lung	GTEx
rs3751325	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs3751325	XRCC6BP1	cis	Stomach	GTEx
rs3751325	XRCC6BP1	cis	Whole Blood	GTEx
rs3751325	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs3751325	XRCC6BP1	cis	multi-tissue	Pritchard
rs3751325	XRCC6BP1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58334400-58335800	Active TSS	Brain Cingulate Gyrus	brain
2	chr12:58334400-58335800	Active TSS	Osteobl	bone
3	chr12:58334400-58336000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr12:58334400-58336000	Active TSS	K562	blood
5	chr12:58334400-58336200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr12:58334400-58336200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:58334400-58336200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr12:58334600-58335800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr12:58334600-58335800	Active TSS	HSMMtube	muscle
10	chr12:58334600-58336000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:58334600-58336000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:58334600-58336000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr12:58334600-58336000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:58334600-58336000	Active TSS	Aorta	Aorta
15	chr12:58334600-58336200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr12:58334600-58336200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr12:58334600-58336200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:58334600-58336200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:58334600-58336200	Active TSS	Fetal Brain Female	brain
20	chr12:58334600-58336200	Active TSS	Fetal Kidney	kidney
21	chr12:58334600-58336200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr12:58334600-58336400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:58334800-58335800	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr12:58334800-58335800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:58334800-58335800	Active TSS	Colon Smooth Muscle	Colon
26	chr12:58334800-58335800	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr12:58334800-58335800	Active TSS	Ovary	ovary
28	chr12:58334800-58335800	Active TSS	GM12878-XiMat	blood
29	chr12:58334800-58336000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:58334800-58336000	Active TSS	Esophagus	oesophagus
31	chr12:58334800-58336000	Active TSS	Gastric	stomach
32	chr12:58334800-58336000	Active TSS	Left Ventricle	heart
33	chr12:58334800-58336000	Active TSS	Lung	lung
34	chr12:58334800-58336000	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr12:58334800-58336000	Active TSS	Small Intestine	intestine
36	chr12:58334800-58336000	Active TSS	HSMM	muscle
37	chr12:58334800-58336200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:58334800-58336200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:58334800-58336200	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr12:58334800-58336200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:58334800-58336200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:58334800-58336200	Active TSS	Brain Angular Gyrus	brain
43	chr12:58334800-58336200	Active TSS	Brain Anterior Caudate	brain
44	chr12:58334800-58336200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:58334800-58336200	Active TSS	Brain Substantia Nigra	brain
46	chr12:58334800-58336200	Active TSS	Pancreas	Pancrea
47	chr12:58334800-58336200	Active TSS	Psoas Muscle	Psoas
48	chr12:58334800-58336200	Active TSS	Right Ventricle	heart
49	chr12:58334800-58336200	Active TSS	A549	lung
50	chr12:58334800-58336400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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