Variant report

Variant	rs11172375
Chromosome Location	chr12:58291574-58291575
allele	C/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	chr12:58291280-58292512	Raji	blood:	n/a	n/a
2	ZNF263	chr12:58290066-58291702	HEK293-T-REx	kidney:	n/a	chr12:58290542-58290551 chr12:58291423-58291444
3	GATA2	chr12:58290796-58291710	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58290453..58292772-chr12:58301540..58304170,2	K562	blood:
2	chr12:58143079..58147361-chr12:58290608..58293518,3	K562	blood:
3	chr12:58239407..58241409-chr12:58290576..58292665,3	MCF-7	breast:
4	chr12:58265896..58267925-chr12:58291113..58293138,2	K562	blood:
5	chr12:58236711..58242486-chr12:58286970..58293951,15	MCF-7	breast:
6	chr12:58257328..58259688-chr12:58290813..58293614,3	MCF-7	breast:
7	chr12:58166094..58167924-chr12:58290124..58292095,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245651	TF binding region
ENSG00000135446	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000257921	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10444569	0.82[ASN][1000 genomes]
rs10877031	0.82[ASN][1000 genomes]
rs10877032	0.82[ASN][1000 genomes]
rs10877033	0.80[ASN][1000 genomes]
rs11172367	0.82[ASN][1000 genomes]
rs11172368	0.81[ASN][1000 genomes]
rs11172369	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11172371	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11172372	0.80[ASN][1000 genomes]
rs11172378	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12319233	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12426201	0.81[ASN][1000 genomes]
rs1599931	0.81[ASN][1000 genomes]
rs1962047	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2002275	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3751330	0.81[ASN][1000 genomes]
rs3751331	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4128707	0.81[ASN][1000 genomes]
rs4237844	0.82[ASN][1000 genomes]
rs4628718	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4630335	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760339	0.82[ASN][1000 genomes]
rs4760341	0.81[ASN][1000 genomes]
rs61935769	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6581157	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6650217	0.81[ASN][1000 genomes]
rs6650218	0.81[ASN][1000 genomes]
rs6650219	0.81[ASN][1000 genomes]
rs7306124	0.83[EUR][1000 genomes]
rs7312623	0.81[ASN][1000 genomes]
rs7954591	0.82[ASN][1000 genomes]
rs7954957	0.82[ASN][1000 genomes]
rs7963992	0.80[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
rs11172375	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs11172375	XRCC6BP1	cis	Whole Blood	GTEx
rs11172375	XRCC6BP1	cis	Artery Tibial	GTEx
rs11172375	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs11172375	XRCC6BP1	cis	Nerve Tibial	GTEx
rs11172375	XRCC6BP1	cis	Artery Aorta	GTEx
rs11172375	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs11172375	XRCC6BP1	cis	lung	GTEx
rs11172375	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs11172375	XRCC6BP1	cis	Thyroid	GTEx
rs11172375	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs11172375	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs11172375	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58288200-58293200	Enhancers	Spleen	Spleen
2	chr12:58288400-58292000	Weak transcription	Hela-S3	cervix
3	chr12:58289200-58293400	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr12:58290200-58292400	Enhancers	Fetal Brain Male	brain
5	chr12:58290200-58293800	Flanking Active TSS	GM12878-XiMat	blood
6	chr12:58290600-58293000	Weak transcription	Gastric	stomach
7	chr12:58290600-58293800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr12:58290600-58293800	Enhancers	HMEC	breast
9	chr12:58290800-58291600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:58290800-58291600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:58290800-58291600	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr12:58290800-58291600	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr12:58290800-58291600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr12:58290800-58291600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr12:58290800-58292200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:58290800-58292400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:58290800-58292400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr12:58290800-58293400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:58290800-58293800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr12:58290800-58294200	Enhancers	Primary B cells from cord blood	blood
21	chr12:58290800-58294200	Enhancers	Primary B cells from peripheral blood	blood
22	chr12:58290800-58294200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:58291000-58291600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:58291000-58291600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:58291000-58291600	Bivalent Enhancer	Thymus	Thymus
26	chr12:58291000-58291800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:58291000-58291800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:58291000-58291800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr12:58291000-58291800	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr12:58291000-58292400	Enhancers	Pancreas	Pancrea
31	chr12:58291000-58292400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr12:58291000-58292600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:58291000-58293000	Enhancers	HSMMtube	muscle
34	chr12:58291000-58293200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr12:58291000-58293200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:58291000-58293200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:58291000-58293200	Enhancers	Fetal Muscle Trunk	muscle
38	chr12:58291000-58293200	Enhancers	Lung	lung
39	chr12:58291000-58293200	Enhancers	Psoas Muscle	Psoas
40	chr12:58291000-58293200	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr12:58291000-58293200	Enhancers	HSMM	muscle
42	chr12:58291000-58293400	Enhancers	Aorta	Aorta
43	chr12:58291000-58293400	Enhancers	Esophagus	oesophagus
44	chr12:58291000-58293400	Enhancers	Left Ventricle	heart
45	chr12:58291000-58293400	Enhancers	K562	blood
46	chr12:58291000-58294000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:58291000-58294000	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr12:58291000-58294000	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr12:58291000-58294200	Enhancers	Fetal Thymus	thymus
50	chr12:58291000-58294400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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