Variant report

Variant	rs62215131
Chromosome Location	chr20:24974607-24974608
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr20:24974122-24974840	MCF-7	breast:	n/a	n/a
2	CTCF	chr20:24972584-24976092	A549	lung:	n/a	n/a
3	RAD21	chr20:24972827-24974927	SK-N-SH	brain:	n/a	chr20:24973647-24973661
4	RFX5	chr20:24974522-24974708	HepG2	liver:	n/a	n/a
5	RAD21	chr20:24974245-24974679	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr20:24974480-24974630	MCF-7	breast:	n/a	n/a
7	CTCF	chr20:24974460-24974610	HAc	cerebellar:	n/a	n/a
8	POLR2A	chr20:24970881-24974631	IMR90	lung:	n/a	n/a
9	RAD21	chr20:24974331-24974654	SK-N-SH_RA	brain:	n/a	n/a
10	POLR2A	chr20:24972739-24974856	GM12878	blood:	n/a	n/a
11	CTCF	chr20:24974155-24974693	MCF-7	breast:	n/a	n/a
12	SMC3	chr20:24974080-24974737	GM12878	blood:	n/a	n/a
13	CTCF	chr20:24974247-24974662	GM12878	blood:	n/a	n/a
14	GABPA	chr20:24972451-24974850	MCF-7	breast:	n/a	n/a
15	SMC3	chr20:24974183-24974763	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr20:24974306-24974628	A549	lung:	n/a	n/a
17	RAD21	chr20:24974152-24974788	HCT-116	colon:	n/a	n/a
18	CTCF	chr20:24974115-24974644	IMR90	lung:	n/a	n/a
19	RAD21	chr20:24974279-24974670	HepG2	liver:	n/a	n/a
20	RAD21	chr20:24974219-24974755	ECC-1	luminal epithelium:	n/a	n/a
21	CTCF	chr20:24974460-24974610	A549	lung:	n/a	n/a
22	RAD21	chr20:24974178-24974735	HepG2	liver:	n/a	n/a
23	MXI1	chr20:24972334-24974826	SK-N-SH	brain:	n/a	n/a
24	RAD21	chr20:24974183-24974739	HCT-116	colon:	n/a	n/a
25	CTCF	chr20:24974480-24974630	HVMF	connective:	n/a	n/a
26	POLR2A	chr20:24972534-24974689	K562	blood:	n/a	n/a
27	RAD21	chr20:24974272-24974612	SK-N-SH_RA	brain:	n/a	n/a
28	CTCF	chr20:24974272-24974762	HCT-116	colon:	n/a	n/a
29	ZNF143	chr20:24974328-24974627	GM12878	blood:	n/a	n/a
30	CTCF	chr20:24974241-24974634	K562	blood:	n/a	n/a
31	POLR2A	chr20:24972485-24974688	GM12891	blood:	n/a	n/a
32	CTCF	chr20:24974109-24974824	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr20:24974221-24974661	HepG2	liver:	n/a	n/a
34	RAD21	chr20:24974277-24974665	HepG2	liver:	n/a	n/a
35	CTCF	chr20:24974460-24974610	HFF-Myc	foreskin:	n/a	n/a
36	RAD21	chr20:24974349-24974621	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr20:24972072-24974726	MCF10A-Er-Src	breast:	n/a	n/a
38	RAD21	chr20:24974310-24974624	A549	lung:	n/a	n/a
39	RAD21	chr20:24974248-24975043	IMR90	lung:	n/a	n/a
40	CTCF	chr20:24974520-24974670	HA-sp	spinal cord:	n/a	n/a
41	MAX	chr20:24972536-24974673	A549	lung:	n/a	n/a
42	CTCF	chr20:24974480-24974630	HBMEC	blood vessel:	n/a	n/a
43	RAD21	chr20:24974203-24974766	MCF-7	breast:	n/a	n/a
44	RAD21	chr20:24974178-24974766	A549	lung:	n/a	n/a
45	CTCF	chr20:24974237-24974677	A549	lung:	n/a	n/a
46	RAD21	chr20:24974216-24974804	A549	lung:	n/a	n/a
47	CTCF	chr20:24974234-24974672	MCF-7	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:24972188..24974753-chr20:24992355..24994002,2	K562	blood:
2	chr20:24970831..24976063-chr20:25037253..25040567,5	MCF-7	breast:
3	chr20:24974463..24977428-chr20:25038810..25041777,2	MCF-7	breast:
4	chr20:24973762..24975336-chr20:25378149..25379762,2	MCF-7	breast:
5	chr20:24974024..24975149-chr20:25046038..25047090,7	MCF-7	breast:
6	chr20:24971936..24974944-chr20:25175039..25178381,3	MCF-7	breast:
7	chr20:24972575..24975462-chr20:25603621..25605250,2	K562	blood:
8	chr20:24974184..24976552-chr20:25044724..25047326,32	MCF-7	breast:
9	chr20:24973677..24976371-chr20:25035249..25037062,2	MCF-7	breast:
10	chr20:24974051..24974784-chr20:25159865..25160396,2	MCF-7	breast:
11	chr20:24974373..24975913-chr20:24978993..24980704,2	MCF-7	breast:

No data

Variant related genes	Relation type
APMAP	TF binding region
ENSG00000170191	Chromatin interaction
ENSG00000154930	Chromatin interaction
ENSG00000213742	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1056033	0.86[ASN][1000 genomes]
rs1056036	0.88[ASN][1000 genomes]
rs11700073	0.97[ASN][1000 genomes]
rs11905625	0.97[ASN][1000 genomes]
rs11906373	0.93[ASN][1000 genomes]
rs12625319	0.84[ASN][1000 genomes]
rs13041643	0.86[ASN][1000 genomes]
rs1331286	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1535042	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854849	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1977540	0.83[ASN][1000 genomes]
rs2008275	0.91[ASN][1000 genomes]
rs2092565	0.86[ASN][1000 genomes]
rs2103736	0.86[ASN][1000 genomes]
rs2151462	0.93[ASN][1000 genomes]
rs2151463	0.93[ASN][1000 genomes]
rs2179729	0.86[ASN][1000 genomes]
rs2179730	0.88[ASN][1000 genomes]
rs2206891	0.82[ASN][1000 genomes]
rs2225459	0.86[ASN][1000 genomes]
rs2235847	0.91[ASN][1000 genomes]
rs227590	0.82[ASN][1000 genomes]
rs227598	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs227613	0.87[ASN][1000 genomes]
rs227614	0.90[ASN][1000 genomes]
rs227615	0.86[ASN][1000 genomes]
rs227616	0.93[ASN][1000 genomes]
rs227618	0.85[ASN][1000 genomes]
rs227619	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227620	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227621	0.93[ASN][1000 genomes]
rs227622	0.93[ASN][1000 genomes]
rs227623	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227624	0.93[ASN][1000 genomes]
rs227625	0.93[ASN][1000 genomes]
rs227626	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227627	0.90[ASN][1000 genomes]
rs227628	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227629	0.93[ASN][1000 genomes]
rs227630	0.93[ASN][1000 genomes]
rs227631	0.93[ASN][1000 genomes]
rs227632	0.93[ASN][1000 genomes]
rs227633	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227634	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227635	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227639	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227643	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227646	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227648	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227649	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs227650	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227651	0.93[ASN][1000 genomes]
rs227652	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227653	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227657	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227658	0.93[ASN][1000 genomes]
rs227659	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2387365	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2387366	0.86[ASN][1000 genomes]
rs2387572	0.86[ASN][1000 genomes]
rs2424691	0.93[ASN][1000 genomes]
rs2892279	0.88[ASN][1000 genomes]
rs34419834	0.86[ASN][1000 genomes]
rs4273288	0.83[ASN][1000 genomes]
rs4527284	0.80[ASN][1000 genomes]
rs4539860	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs45468392	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45556041	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4813541	0.86[ASN][1000 genomes]
rs4813542	0.86[ASN][1000 genomes]
rs4815327	0.83[ASN][1000 genomes]
rs4815337	0.86[ASN][1000 genomes]
rs4815339	0.84[ASN][1000 genomes]
rs4815340	0.86[ASN][1000 genomes]
rs4815341	0.88[ASN][1000 genomes]
rs4815351	0.82[ASN][1000 genomes]
rs4815355	0.86[ASN][1000 genomes]
rs4815357	0.91[ASN][1000 genomes]
rs56312312	0.97[ASN][1000 genomes]
rs57265446	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58244398	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036976	0.83[ASN][1000 genomes]
rs6050118	0.80[AMR][1000 genomes]
rs6050131	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050134	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6050177	0.88[ASN][1000 genomes]
rs6050179	0.88[ASN][1000 genomes]
rs6050181	0.88[ASN][1000 genomes]
rs6050201	0.88[ASN][1000 genomes]
rs6083684	0.86[ASN][1000 genomes]
rs6083685	0.86[ASN][1000 genomes]
rs6083686	0.86[ASN][1000 genomes]
rs6083688	0.86[ASN][1000 genomes]
rs6083692	0.84[ASN][1000 genomes]
rs6083699	0.86[ASN][1000 genomes]
rs6083709	0.91[ASN][1000 genomes]
rs6106975	0.88[ASN][1000 genomes]
rs6106984	0.97[ASN][1000 genomes]
rs6114980	0.97[ASN][1000 genomes]
rs6114981	0.97[ASN][1000 genomes]
rs6114984	0.97[ASN][1000 genomes]
rs6114988	0.97[ASN][1000 genomes]
rs6132773	0.86[ASN][1000 genomes]
rs6132774	0.86[ASN][1000 genomes]
rs6132775	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132777	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132778	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132784	0.81[ASN][1000 genomes]
rs6138417	0.86[ASN][1000 genomes]
rs6138423	0.86[ASN][1000 genomes]
rs6138431	0.80[ASN][1000 genomes]
rs6138435	0.86[ASN][1000 genomes]
rs6138437	0.86[ASN][1000 genomes]
rs6138438	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138453	0.91[ASN][1000 genomes]
rs6138455	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138456	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138457	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138458	0.97[ASN][1000 genomes]
rs6138460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138461	0.85[ASN][1000 genomes]
rs6138463	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138465	0.81[ASN][1000 genomes]
rs62215110	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62215115	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62215128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707	0.90[ASN][1000 genomes]
rs7268095	0.97[ASN][1000 genomes]
rs7269416	0.97[ASN][1000 genomes]
rs735886	0.86[ASN][1000 genomes]
rs8125909	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8183891	0.91[ASN][1000 genomes]
rs914314	0.85[ASN][1000 genomes]
rs926661	0.88[ASN][1000 genomes]
rs926662	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv2762068	chr20:24908860-24974986	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62215131	CST7	cis	Whole Blood	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24973800-24974800	Flanking Active TSS	HepG2	liver
2	chr20:24973800-24975200	Weak transcription	Gastric	stomach
3	chr20:24973800-24975400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:24973800-24975800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:24973800-24975800	Weak transcription	Lung	lung
6	chr20:24974000-24974800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr20:24974000-24974800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr20:24974000-24974800	Weak transcription	Colonic Mucosa	Colon
9	chr20:24974000-24974800	Enhancers	Fetal Kidney	kidney
10	chr20:24974000-24974800	Enhancers	Fetal Stomach	stomach
11	chr20:24974000-24974800	Enhancers	HUVEC	blood vessel
12	chr20:24974000-24975000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:24974000-24975000	Weak transcription	Left Ventricle	heart
14	chr20:24974000-24975000	Weak transcription	Stomach Mucosa	stomach
15	chr20:24974000-24975200	Weak transcription	Brain Germinal Matrix	brain
16	chr20:24974000-24975200	Weak transcription	Ovary	ovary
17	chr20:24974000-24975200	Weak transcription	Right Ventricle	heart
18	chr20:24974000-24975200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr20:24974000-24975600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr20:24974000-24975600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr20:24974000-24975600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr20:24974000-24975600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr20:24974000-24975800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr20:24974000-24975800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr20:24974000-24975800	Weak transcription	HSMMtube	muscle
26	chr20:24974000-24976000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr20:24974000-24976000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr20:24974000-24976200	Enhancers	Primary B cells from peripheral blood	blood
29	chr20:24974000-24976200	Enhancers	Primary T cells fromperipheralblood	blood
30	chr20:24974000-24976200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:24974000-24976200	Enhancers	Fetal Intestine Small	intestine
32	chr20:24974000-24976400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr20:24974000-24976400	Enhancers	Fetal Thymus	thymus
34	chr20:24974000-24976600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr20:24974000-24976800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr20:24974000-24976800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr20:24974000-24977000	Enhancers	Fetal Muscle Leg	muscle
38	chr20:24974000-24977800	Enhancers	Placenta	Placenta
39	chr20:24974000-24979000	Enhancers	Duodenum Mucosa	Duodenum
40	chr20:24974000-24981000	Weak transcription	Psoas Muscle	Psoas
41	chr20:24974000-24985800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr20:24974000-24985800	Weak transcription	Thymus	Thymus
43	chr20:24974000-24986400	Weak transcription	Aorta	Aorta
44	chr20:24974200-24974800	Enhancers	NH-A	brain
45	chr20:24974200-24975000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr20:24974200-24975200	Weak transcription	Fetal Intestine Large	intestine
47	chr20:24974200-24975400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr20:24974200-24975400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr20:24974200-24975400	Enhancers	K562	blood
50	chr20:24974200-24975600	Weak transcription	Primary hematopoietic stem cells	blood

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