Variant report

Variant	rs2255651
Chromosome Location	chr20:1513842-1513843
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	CTCF	chr20:1513801-1514118	HepG2	liver:	n/a	chr20:1513907-1513923
2	RAD21	chr20:1513794-1514102	SK-N-SH_RA	brain:	n/a	n/a
3	SMC3	chr20:1513779-1514052	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr20:1513800-1513950	AG09309	skin:	n/a	chr20:1513907-1513923
5	CTCF	chr20:1513760-1513910	SAEC	small airway:	n/a	n/a
6	RAD21	chr20:1513791-1513996	SK-N-SH_RA	brain:	n/a	n/a
7	RAD21	chr20:1513699-1514167	MCF-7	breast:	n/a	n/a
8	CTCF	chr20:1513800-1513950	HMEC	breast:	n/a	chr20:1513907-1513923
9	CTCF	chr20:1513780-1513930	GM12869	blood:	n/a	chr20:1513907-1513923
10	RAD21	chr20:1513779-1514201	A549	lung:	n/a	n/a
11	CTCF	chr20:1513809-1514031	MCF-7	breast:	n/a	chr20:1513907-1513923
12	CTCF	chr20:1513742-1514092	GM12878	blood:	n/a	chr20:1513907-1513923
13	CTCF	chr20:1513826-1514011	GM12878	blood:	n/a	chr20:1513907-1513923
14	RAD21	chr20:1513787-1514050	HepG2	liver:	n/a	n/a
15	CTCF	chr20:1513736-1513969	A549	lung:	n/a	chr20:1513907-1513923
16	CTCF	chr20:1513820-1513970	GM12871	blood:	n/a	chr20:1513907-1513923
17	CTCF	chr20:1513835-1514014	HepG2	liver:	n/a	chr20:1513907-1513923
18	CTCF	chr20:1513800-1513950	GM12873	blood:	n/a	chr20:1513907-1513923
19	CTCF	chr20:1513840-1513990	GM12873	blood:	n/a	chr20:1513907-1513923
20	RAD21	chr20:1513793-1514077	GM12878	blood:	n/a	n/a
21	CTCF	chr20:1513780-1513930	RPTEC	kidney:	n/a	chr20:1513907-1513923
22	CTCF	chr20:1513800-1513950	Hela-S3	cervix:	n/a	chr20:1513907-1513923
23	CTCF	chr20:1513780-1513930	HEEpiC	esophagus:	n/a	chr20:1513907-1513923
24	CTCF	chr20:1513819-1514009	Hela-S3	cervix:	n/a	chr20:1513907-1513923
25	CTCF	chr20:1513840-1513990	GM12874	blood:	n/a	chr20:1513907-1513923
26	SMC3	chr20:1513777-1514095	GM12878	blood:	n/a	n/a
27	CTCF	chr20:1513820-1513970	GM12874	blood:	n/a	chr20:1513907-1513923
28	CTCF	chr20:1513834-1513989	LNCaP	prostate:	n/a	chr20:1513907-1513923
29	CTCF	chr20:1513820-1513970	HepG2	liver:	n/a	chr20:1513907-1513923
30	CTCF	chr20:1513840-1513990	NB4	blood:	n/a	chr20:1513907-1513923
31	CTCF	chr20:1513800-1513950	GM12864	blood:	n/a	chr20:1513907-1513923
32	RAD21	chr20:1513715-1514115	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr20:1513840-1513990	GM12872	blood:	n/a	chr20:1513907-1513923
34	RAD21	chr20:1513711-1514192	A549	lung:	n/a	n/a
35	CTCF	chr20:1513834-1514054	A549	lung:	n/a	chr20:1513907-1513923
36	CTCF	chr20:1513820-1513970	HEK293	kidney:	n/a	chr20:1513907-1513923
37	CTCF	chr20:1513800-1513950	HUVEC	blood vessel:	n/a	chr20:1513907-1513923
38	RAD21	chr20:1513686-1514208	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr20:1513828-1513988	GM12878	blood:	n/a	n/a
40	CTCF	chr20:1513799-1514025	H1-hESC	embryonic stem cell:	n/a	chr20:1513907-1513923
41	CTCF	chr20:1513840-1513990	A549	lung:	n/a	chr20:1513907-1513923
42	CTCF	chr20:1513820-1513970	GM12870	blood:	n/a	chr20:1513907-1513923
43	CTCF	chr20:1513800-1513950	K562	blood:	n/a	chr20:1513907-1513923
44	RAD21	chr20:1513770-1514111	GM12878	blood:	n/a	n/a
45	CTCF	chr20:1513820-1513970	MCF-7	breast:	n/a	chr20:1513907-1513923
46	RAD21	chr20:1513741-1514122	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr20:1513780-1513930	GM12871	blood:	n/a	chr20:1513907-1513923
48	RAD21	chr20:1513794-1514041	HepG2	liver:	n/a	n/a
49	CTCF	chr20:1513820-1513970	HMF	breast:	n/a	chr20:1513907-1513923
50	CTCF	chr20:1513818-1514013	HUVEC	blood vessel:	n/a	chr20:1513907-1513923

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1513747..1514348-chr20:1714921..1715422,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-917P	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2224878	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2249431	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249832	1.00[JPT][hapmap]
rs2250055	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250091	1.00[JPT][hapmap]
rs2252400	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2252401	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2252425	1.00[ASN][1000 genomes]
rs2253429	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2253431	0.84[ASN][1000 genomes]
rs2253693	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2253698	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2253815	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2253821	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255641	1.00[CEU][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255988	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256095	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2256229	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2256240	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2256243	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2256250	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2256251	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2263654	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2263656	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2263660	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263663	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422609	0.92[ASN][1000 genomes]
rs2422613	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2422614	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422617	0.84[ASN][1000 genomes]
rs2422618	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074896	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7264491	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2758509	chr20:1476781-1679256	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2758777	chr20:1476781-1679256	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv428374	chr20:1476781-1679256	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1057036	chr20:1493425-1869281	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv912597	chr20:1500506-1877150	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv510779	chr20:1509330-1613962	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2255651	C20orf141	cis	parietal	SCAN
rs2255651	TMC2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1508000-1515200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr20:1513600-1514000	Enhancers	NHEK	skin
3	chr20:1513800-1514800	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr20:1513800-1516400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr20:1513800-1517200	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links