Variant report

Variant	rs10877024
Chromosome Location	chr12:58226709-58226710
allele	C/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	SMC3	chr12:58226676-58226850	GM12878	blood:	n/a	n/a
2	FOXM1	chr12:58226667-58227094	GM12878	blood:	n/a	n/a
3	CHD1	chr12:58226698-58226841	GM12878	blood:	n/a	n/a
4	MTA3	chr12:58226516-58227362	GM12878	blood:	n/a	n/a
5	MTA3	chr12:58226633-58227098	GM12878	blood:	n/a	n/a
6	NFIC	chr12:58226541-58227133	GM12878	blood:	n/a	n/a
7	TBL1XR1	chr12:58226704-58226909	GM12878	blood:	n/a	n/a
8	RUNX3	chr12:58226610-58227178	GM12878	blood:	n/a	chr12:58227137-58227146
9	ZNF384	chr12:58226492-58226729	GM12878	blood:	n/a	n/a
10	RUNX3	chr12:58226518-58227273	GM12878	blood:	n/a	chr12:58227137-58227146

No.	Distal block	Cell Line	Cell type
1	chr12:58225758..58227356-chr12:58293010..58294775,2	MCF-7	breast:
2	chr12:58224317..58226991-chr12:58298753..58300053,48	MCF-7	breast:
3	chr12:58225549..58227455-chr12:58294861..58299199,3	MCF-7	breast:
4	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: 43 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10444569	0.87[AMR][1000 genomes]
rs10747784	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10783850	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783851	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783854	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10783855	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10783856	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10877022	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877025	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877026	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877029	0.81[AMR][1000 genomes]
rs10877030	0.81[AMR][1000 genomes]
rs10877031	0.87[AMR][1000 genomes]
rs10877032	0.82[AMR][1000 genomes]
rs11172361	0.81[EUR][1000 genomes]
rs11172362	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172367	0.82[AMR][1000 genomes]
rs11172368	0.80[AMR][1000 genomes]
rs11172369	0.83[AMR][1000 genomes]
rs11172371	0.81[AMR][1000 genomes]
rs12312955	0.84[AMR][1000 genomes]
rs12319233	0.84[AMR][1000 genomes]
rs12426201	0.87[AMR][1000 genomes]
rs1599750	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1599751	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1599931	0.86[AMR][1000 genomes]
rs1875125	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002275	0.82[AMR][1000 genomes]
rs4237844	0.87[AMR][1000 genomes]
rs4760171	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760172	0.81[AMR][1000 genomes]
rs4760332	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760333	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760335	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4760339	0.87[AMR][1000 genomes]
rs4760341	0.84[AMR][1000 genomes]
rs5017863	0.86[AMR][1000 genomes]
rs7134797	0.81[AMR][1000 genomes]
rs7312623	0.87[AMR][1000 genomes]
rs7489290	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs870392	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs871871	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10877024	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10877024	METTL21B	cis	Esophagus Muscularis	GTEx
rs10877024	XRCC6BP1	cis	Artery Tibial	GTEx
rs10877024	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10877024	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs10877024	XRCC6BP1	cis	lung	GTEx
rs10877024	XRCC6BP1	cis	Whole Blood	GTEx
rs10877024	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877024	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10877024	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10877024	METTL21B	cis	Whole Blood	GTEx
rs10877024	METTL21B	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58209400-58226800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:58215400-58227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:58222800-58230200	Enhancers	Right Atrium	heart
4	chr12:58222800-58230400	Genic enhancers	Fetal Stomach	stomach
5	chr12:58223000-58228400	Genic enhancers	Fetal Thymus	thymus
6	chr12:58223000-58230400	Genic enhancers	Fetal Muscle Leg	muscle
7	chr12:58223400-58226800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:58223400-58230400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:58223400-58231000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:58223400-58236400	Enhancers	Right Ventricle	heart
11	chr12:58223600-58226800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr12:58223600-58230400	Weak transcription	Hela-S3	cervix
13	chr12:58223600-58231600	Enhancers	Placenta	Placenta
14	chr12:58223800-58226800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:58223800-58230800	Enhancers	Liver	Liver
16	chr12:58224000-58230200	Weak transcription	Dnd41	blood
17	chr12:58224200-58230600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:58224200-58238200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:58224400-58238000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:58224400-58238200	Enhancers	Spleen	Spleen
21	chr12:58224800-58226800	Weak transcription	Brain Germinal Matrix	brain
22	chr12:58224800-58227800	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr12:58224800-58229600	Enhancers	Primary B cells from peripheral blood	blood
24	chr12:58225000-58227600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr12:58225000-58228000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:58225000-58230200	Enhancers	Fetal Heart	heart
27	chr12:58225200-58228400	Enhancers	Osteobl	bone
28	chr12:58225200-58237000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr12:58225400-58227200	Enhancers	HSMMtube	muscle
30	chr12:58225400-58227400	Enhancers	HUVEC	blood vessel
31	chr12:58225400-58227800	Enhancers	Fetal Kidney	kidney
32	chr12:58225400-58235600	Genic enhancers	Fetal Intestine Small	intestine
33	chr12:58225600-58228600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:58225600-58228600	Genic enhancers	Fetal Lung	lung
35	chr12:58225600-58229800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr12:58225600-58232800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:58225600-58238200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:58225800-58226800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:58225800-58226800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr12:58225800-58226800	Enhancers	Primary B cells from cord blood	blood
41	chr12:58225800-58226800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:58225800-58226800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr12:58225800-58227000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:58225800-58227200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:58225800-58227400	Weak transcription	HepG2	liver
46	chr12:58225800-58228000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:58225800-58229200	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr12:58225800-58229200	Enhancers	Primary T cells from cord blood	blood
49	chr12:58225800-58229200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr12:58225800-58229400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links