Variant report

Variant	rs1875125
Chromosome Location	chr12:58227241-58227242
allele	G/T
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	chr12:58227133-58227491	H1-hESC	embryonic stem cell:	n/a	n/a
2	MTA3	chr12:58226516-58227362	GM12878	blood:	n/a	n/a
3	TBP	chr12:58227185-58227289	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:58226865-58227435	HepG2	liver:	n/a	n/a
5	RUNX3	chr12:58226518-58227273	GM12878	blood:	n/a	chr12:58227137-58227146
6	ZNF143	chr12:58226895-58227519	H1-hESC	embryonic stem cell:	n/a	n/a
7	WRNIP1	chr12:58226831-58228537	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58225758..58227356-chr12:58293010..58294775,2	MCF-7	breast:
2	chr12:58225549..58227455-chr12:58294861..58299199,3	MCF-7	breast:
3	chr12:58225399..58227620-chr12:58230224..58232675,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257953	TF binding region
CTDSP2	TF binding region
ENSG00000257953	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1021469	0.83[JPT][hapmap]
rs10431552	0.88[JPT][hapmap]
rs10444569	0.86[AMR][1000 genomes]
rs10747783	0.89[JPT][hapmap]
rs10747784	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10747786	0.94[JPT][hapmap]
rs10747787	0.94[JPT][hapmap]
rs10783847	0.88[JPT][hapmap]
rs10783848	0.88[JPT][hapmap]
rs10783850	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783851	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783853	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10783854	0.85[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10783855	0.85[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10783856	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10877011	1.00[YRI][hapmap]
rs10877012	0.88[JPT][hapmap]
rs10877013	0.81[JPT][hapmap]
rs10877014	0.88[JPT][hapmap]
rs10877015	0.88[JPT][hapmap]
rs10877016	0.88[JPT][hapmap]
rs10877019	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs10877022	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877024	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877025	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877026	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877028	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs10877029	0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs10877030	0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs10877031	0.86[AMR][1000 genomes]
rs10877032	0.81[AMR][1000 genomes]
rs11172333	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs11172335	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs11172343	0.89[JPT][hapmap];0.87[YRI][hapmap]
rs11172344	0.88[JPT][hapmap]
rs11172349	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs11172351	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs11172361	0.81[EUR][1000 genomes]
rs11172362	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172367	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs11172369	0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs11172371	0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs12312955	0.83[AMR][1000 genomes]
rs12319233	0.83[AMR][1000 genomes]
rs12426201	0.86[AMR][1000 genomes]
rs1599750	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1599751	0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1599931	0.94[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes]
rs1875124	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs2002275	0.83[AMR][1000 genomes]
rs2069502	0.83[JPT][hapmap];0.85[YRI][hapmap]
rs2072052	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs3825079	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs4237844	0.94[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes]
rs4646536	0.88[JPT][hapmap]
rs4760171	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760172	0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs4760332	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760333	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760335	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4760339	0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs4760341	0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs5017863	0.87[AMR][1000 genomes]
rs6581155	0.88[JPT][hapmap]
rs703842	0.88[JPT][hapmap]
rs7134797	0.80[AMR][1000 genomes]
rs724834	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs7312623	0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs7489290	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8181644	0.88[JPT][hapmap]
rs870392	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs871871	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs923829	0.89[JPT][hapmap]

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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1875125	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs1875125	XRCC6BP1	cis	lung	GTEx
rs1875125	XRCC6BP1	cis	Whole Blood	GTEx
rs1875125	FAM119B	cis	Temporal Cortex	GTEx
rs1875125	DKFZP586D0919	cis	multi-tissue	Pritchard
rs1875125	FAM119B	cis	Frontal Cortex	GTEx
rs1875125	XRCC6BP1	cis	Artery Tibial	GTEx
rs1875125	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs1875125	FAM119B	cis	Cerebellum	GTEx
rs1875125	FAM119B	cis	Lymphoblastoid	GTEx
rs1875125	METTL21B	cis	Whole Blood	GTEx
rs1875125	METTL21B	cis	Esophagus Muscularis	GTEx
rs1875125	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1875125	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs1875125	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs1875125	METTL21B	cis	Muscle Skeletal	GTEx
rs1875125	FAM119B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58222800-58230200	Enhancers	Right Atrium	heart
2	chr12:58222800-58230400	Genic enhancers	Fetal Stomach	stomach
3	chr12:58223000-58228400	Genic enhancers	Fetal Thymus	thymus
4	chr12:58223000-58230400	Genic enhancers	Fetal Muscle Leg	muscle
5	chr12:58223400-58230400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:58223400-58231000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:58223400-58236400	Enhancers	Right Ventricle	heart
8	chr12:58223600-58230400	Weak transcription	Hela-S3	cervix
9	chr12:58223600-58231600	Enhancers	Placenta	Placenta
10	chr12:58223800-58230800	Enhancers	Liver	Liver
11	chr12:58224000-58230200	Weak transcription	Dnd41	blood
12	chr12:58224200-58230600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:58224200-58238200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:58224400-58238000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:58224400-58238200	Enhancers	Spleen	Spleen
16	chr12:58224800-58227800	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr12:58224800-58229600	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:58225000-58227600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr12:58225000-58228000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:58225000-58230200	Enhancers	Fetal Heart	heart
21	chr12:58225200-58228400	Enhancers	Osteobl	bone
22	chr12:58225200-58237000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr12:58225400-58227400	Enhancers	HUVEC	blood vessel
24	chr12:58225400-58227800	Enhancers	Fetal Kidney	kidney
25	chr12:58225400-58235600	Genic enhancers	Fetal Intestine Small	intestine
26	chr12:58225600-58228600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:58225600-58228600	Genic enhancers	Fetal Lung	lung
28	chr12:58225600-58229800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr12:58225600-58232800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:58225600-58238200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:58225800-58227400	Weak transcription	HepG2	liver
32	chr12:58225800-58228000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:58225800-58229200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr12:58225800-58229200	Enhancers	Primary T cells from cord blood	blood
35	chr12:58225800-58229200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr12:58225800-58229400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:58225800-58229400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr12:58225800-58229400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr12:58225800-58229400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:58225800-58229400	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr12:58225800-58229600	Enhancers	Primary hematopoietic stem cells	blood
42	chr12:58225800-58229600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr12:58225800-58229800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr12:58225800-58229800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr12:58225800-58230000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:58225800-58230400	Weak transcription	A549	lung
47	chr12:58225800-58230600	Enhancers	Thymus	Thymus
48	chr12:58225800-58236000	Enhancers	Brain Angular Gyrus	brain
49	chr12:58226000-58227400	Enhancers	Brain Anterior Caudate	brain
50	chr12:58226000-58227400	Enhancers	Brain Cingulate Gyrus	brain

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