Variant report

Variant	rs4760171
Chromosome Location	chr12:58225904-58225905
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	CTCF	chr12:58224998-58226023	SK-N-SH	brain:	n/a	chr12:58225332-58225353 chr12:58225331-58225347 chr12:58225333-58225346 chr12:58225330-58225348 chr12:58225871-58225879
2	CTCF	chr12:58225062-58226021	HCT-116	colon:	n/a	chr12:58225332-58225353 chr12:58225331-58225347 chr12:58225333-58225346 chr12:58225330-58225348 chr12:58225871-58225879
3	RAD21	chr12:58225883-58226040	HepG2	liver:	n/a	n/a
4	KAP1	chr12:58225245-58225927	HEK293	kidney:	n/a	n/a
5	RCOR1	chr12:58225160-58225956	K562	blood:	n/a	n/a
6	SMC3	chr12:58224982-58226412	SK-N-SH	brain:	n/a	chr12:58225332-58225346
7	RAD21	chr12:58224921-58226115	SK-N-SH	brain:	n/a	chr12:58225331-58225350 chr12:58225871-58225885 chr12:58225332-58225346
8	SMC3	chr12:58225090-58225913	Hela-S3	cervix:	n/a	chr12:58225332-58225346
9	CTCF	chr12:58224939-58226122	A549	lung:	n/a	chr12:58225332-58225353 chr12:58225331-58225347 chr12:58225333-58225346 chr12:58225330-58225348 chr12:58225871-58225879

No.	Distal block	Cell Line	Cell type
1	chr12:58224846..58226357-chr12:58288435..58290934,2	K562	blood:
2	chr12:58224966..58226031-chr12:58290315..58291164,3	MCF-7	breast:
3	chr12:58225758..58227356-chr12:58293010..58294775,2	MCF-7	breast:
4	chr12:58196770..58197708-chr12:58225211..58225923,2	MCF-7	breast:
5	chr12:58224418..58226286-chr12:58298796..58299791,24	MCF-7	breast:
6	chr12:58224470..58226118-chr12:58290368..58291505,5	MCF-7	breast:
7	chr12:58224317..58226991-chr12:58298753..58300053,48	MCF-7	breast:
8	chr12:58225549..58227455-chr12:58294861..58299199,3	MCF-7	breast:
9	chr12:58224854..58226524-chr12:58298322..58299858,37	K562	blood:
10	chr12:58225399..58227620-chr12:58230224..58232675,3	MCF-7	breast:

Variant related genes	Relation type
CTDSP2	TF binding region
ENSG00000257953	TF binding region
ENSG00000245651	Chromatin interaction
ENSG00000257953	Chromatin interaction
ENSG00000270039	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10431552	0.83[JPT][hapmap]
rs10747783	0.83[JPT][hapmap]
rs10747784	0.81[EUR][1000 genomes]
rs10747786	0.84[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs10747787	0.84[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs10783847	0.83[JPT][hapmap];0.82[MKK][hapmap];0.90[YRI][hapmap]
rs10783848	0.80[JPT][hapmap]
rs10783850	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10783851	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783854	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10783855	0.88[CEU][hapmap];0.90[CHD][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10783856	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10877012	0.83[JPT][hapmap]
rs10877014	0.83[JPT][hapmap]
rs10877015	0.83[JPT][hapmap]
rs10877016	0.83[JPT][hapmap]
rs10877019	0.83[JPT][hapmap]
rs10877022	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877024	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877025	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877026	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10877028	0.81[ASW][hapmap];0.88[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs10877029	0.91[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs10877030	0.91[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs11172333	0.83[JPT][hapmap]
rs11172335	0.83[JPT][hapmap]
rs11172343	0.83[JPT][hapmap]
rs11172344	0.83[JPT][hapmap];0.88[MKK][hapmap];0.90[YRI][hapmap]
rs11172349	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs11172351	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs11172361	0.81[EUR][1000 genomes]
rs11172362	0.81[EUR][1000 genomes]
rs11172367	0.84[GIH][hapmap];0.87[JPT][hapmap]
rs11172369	0.87[JPT][hapmap]
rs1599750	0.87[ASW][hapmap];0.88[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1599751	0.80[ASW][hapmap];0.88[CEU][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1599931	0.86[JPT][hapmap]
rs1875124	0.83[JPT][hapmap]
rs1875125	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]
rs3825079	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs4237844	0.87[JPT][hapmap]
rs4646536	0.83[JPT][hapmap]
rs4760172	0.80[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs4760332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760333	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760335	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4760339	0.86[JPT][hapmap]
rs4760341	0.87[JPT][hapmap]
rs6581155	0.83[JPT][hapmap]
rs703842	0.83[JPT][hapmap]
rs724834	0.83[JPT][hapmap]
rs7312623	0.87[JPT][hapmap]
rs7489290	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8181644	0.83[JPT][hapmap]
rs870392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs871871	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs923829	0.83[JPT][hapmap];0.90[YRI][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:31)

SNP	Gene	Cis/trans	Tissue	Source
rs4760171	XRCC6BP1	cis	Artery Tibial	GTEx
rs4760171	MUCL1	cis	parietal	SCAN
rs4760171	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs4760171	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs4760171	XRCC6BP1	cis	multi-tissue	Pritchard
rs4760171	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760171	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4760171	CDK2	cis	parietal	SCAN
rs4760171	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs4760171	FAM119B	cis	Cerebellum	GTEx
rs4760171	METTL21B	cis	Esophagus Muscularis	GTEx
rs4760171	DKFZP586D0919	cis	multi-tissue	Pritchard
rs4760171	GPR84	cis	cerebellum	SCAN
rs4760171	TSPAN31	cis	cerebellum	SCAN
rs4760171	XRCC6BP1	cis	Whole Blood	GTEx
rs4760171	FAM119B	cis	Frontal Cortex	GTEx
rs4760171	FAM119B	cis	Lymphoblastoid	GTEx
rs4760171	FAM119B	cis	cerebellum	SCAN
rs4760171	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs4760171	METTL21B	cis	Muscle Skeletal	GTEx
rs4760171	FAM119B	cis	parietal	SCAN
rs4760171	XRCC6BP1	cis	lung	GTEx
rs4760171	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs4760171	TSFM	cis	multi-tissue	Pritchard
rs4760171	TSFM	cis	lymphoblastoid	seeQTL
rs4760171	FAM119B	cis	Temporal Cortex	GTEx
rs4760171	METTL21B	cis	Whole Blood	GTEx
rs4760171	PPP1R1A	cis	parietal	SCAN
rs4760171	TSFM	cis	cerebellum	SCAN
rs4760171	FAM119B	cis	lymphoblastoid	seeQTL
rs4760171	TSPAN31	cis	parietal	SCAN

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	chr12:58223400-58226200	Enhancers	Ovary	ovary
8	chr12:58223400-58226200	Enhancers	Psoas Muscle	Psoas
9	chr12:58223400-58226800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:58223400-58230400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:58223400-58231000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:58223400-58236400	Enhancers	Right Ventricle	heart
13	chr12:58223600-58226000	Enhancers	Left Ventricle	heart
14	chr12:58223600-58226800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr12:58223600-58230400	Weak transcription	Hela-S3	cervix
16	chr12:58223600-58231600	Enhancers	Placenta	Placenta
17	chr12:58223800-58226800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:58223800-58230800	Enhancers	Liver	Liver
19	chr12:58224000-58226400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:58224000-58230200	Weak transcription	Dnd41	blood
21	chr12:58224200-58230600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:58224200-58238200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:58224400-58238000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:58224400-58238200	Enhancers	Spleen	Spleen
25	chr12:58224800-58226200	Enhancers	Lung	lung
26	chr12:58224800-58226800	Weak transcription	Brain Germinal Matrix	brain
27	chr12:58224800-58227800	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr12:58224800-58229600	Enhancers	Primary B cells from peripheral blood	blood
29	chr12:58225000-58226000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:58225000-58226000	Flanking Active TSS	Colonic Mucosa	Colon
31	chr12:58225000-58226000	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr12:58225000-58226000	Enhancers	Gastric	stomach
33	chr12:58225000-58226000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr12:58225000-58226000	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr12:58225000-58226200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:58225000-58226200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:58225000-58226200	Enhancers	Aorta	Aorta
38	chr12:58225000-58226200	Enhancers	Pancreas	Pancrea
39	chr12:58225000-58226200	Enhancers	Small Intestine	intestine
40	chr12:58225000-58226400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr12:58225000-58226400	Enhancers	Stomach Mucosa	stomach
42	chr12:58225000-58227600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr12:58225000-58228000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:58225000-58230200	Enhancers	Fetal Heart	heart
45	chr12:58225200-58226000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr12:58225200-58226000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:58225200-58226000	Enhancers	Fetal Intestine Large	intestine
48	chr12:58225200-58226000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr12:58225200-58226200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr12:58225200-58228400	Enhancers	Osteobl	bone

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