Variant report

Variant	rs62116419
Chromosome Location	chr19:51976582-51976583
allele	A/C
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	EP300	chr19:51976198-51976677	K562	blood:	n/a	n/a
2	RAD21	chr19:51976038-51976770	HCT-116	colon:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
3	POLR2A	chr19:51976159-51977200	K562	blood:	n/a	n/a
4	RAD21	chr19:51976141-51976596	MCF-7	breast:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
5	RAD21	chr19:51976174-51976585	IMR90	lung:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
6	RAD21	chr19:51976137-51976615	A549	lung:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
7	RAD21	chr19:51976141-51976625	MCF-7	breast:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
8	ARID3A	chr19:51976233-51976587	K562	blood:	n/a	n/a
9	CTCF	chr19:51975842-51976738	SK-N-SH	brain:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
10	IRF1	chr19:51975954-51976586	K562	blood:	n/a	n/a
11	RAD21	chr19:51976194-51976613	GM12878	blood:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
12	CTCF	chr19:51976136-51976620	MCF-7	breast:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
13	SMC3	chr19:51975997-51976802	SK-N-SH	brain:	n/a	chr19:51976564-51976578 chr19:51976363-51976377 chr19:51976363-51976371
14	ZMIZ1	chr19:51975969-51976618	K562	blood:	n/a	n/a
15	SMC3	chr19:51976120-51976623	GM12878	blood:	n/a	chr19:51976564-51976578 chr19:51976363-51976377 chr19:51976363-51976371
16	RAD21	chr19:51976236-51976641	ECC-1	luminal epithelium:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
17	MAZ	chr19:51976214-51976585	K562	blood:	n/a	n/a
18	CTCF	chr19:51976153-51976633	A549	lung:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
19	JUN	chr19:51976291-51976604	K562	blood:	n/a	n/a
20	CTCF	chr19:51976050-51976707	K562	blood:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
21	CTCF	chr19:51976116-51976631	K562	blood:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
22	RAD21	chr19:51976142-51976587	GM12878	blood:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
23	CTCF	chr19:51976148-51976586	GM12878	blood:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
24	TBL1XR1	chr19:51976165-51976592	K562	blood:	n/a	n/a
25	SMC3	chr19:51976193-51976632	K562	blood:	n/a	chr19:51976564-51976578 chr19:51976363-51976377 chr19:51976363-51976371
26	CTCF	chr19:51976080-51976703	MCF-7	breast:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
27	RAD21	chr19:51976188-51976590	Hela-S3	cervix:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
28	REST	chr19:51976118-51976700	HL-60	blood:	n/a	n/a
29	RAD21	chr19:51976166-51976678	A549	lung:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
30	RAD21	chr19:51975976-51976681	SK-N-SH	brain:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
31	CTCF	chr19:51976100-51976587	HepG2	liver:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
32	RAD21	chr19:51976120-51976606	H1-hESC	embryonic stem cell:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
33	CTCF	chr19:51975966-51976935	A549	lung:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
34	CTCF	chr19:51976079-51976745	HCT-116	colon:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
35	RAD21	chr19:51976151-51976670	HepG2	liver:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
36	BHLHE40	chr19:51976238-51976595	K562	blood:	n/a	n/a
37	REST	chr19:51976226-51976584	K562	blood:	n/a	n/a
38	CTCF	chr19:51976123-51976586	K562	blood:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
39	RAD21	chr19:51976018-51976679	HCT-116	colon:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
40	RAD21	chr19:51976251-51976591	ECC-1	luminal epithelium:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
41	CTCF	chr19:51976011-51976785	HCT-116	colon:	n/a	chr19:51976363-51976384 chr19:51976562-51976580 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976557-51976578 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377 chr19:51976563-51976579
42	SMC3	chr19:51976187-51976608	HepG2	liver:	n/a	chr19:51976564-51976578 chr19:51976363-51976377 chr19:51976363-51976371
43	ZC3H11A	chr19:51976093-51976621	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51976019..51976960-chr19:52110904..52111829,3	MCF-7	breast:
2	chr19:51976250..51976763-chr19:52286398..52287255,2	MCF-7	breast:
3	chr19:51975672..51976584-chr19:52164011..52164572,3	MCF-7	breast:
4	chr19:51975890..51976812-chr19:52159933..52160756,4	K562	blood:
5	chr19:51975913..51977254-chr19:52159906..52161263,12	MCF-7	breast:
6	chr19:51975937..51976795-chr19:52018276..52018797,2	MCF-7	breast:
7	chr19:51975813..51976889-chr19:52140105..52142089,6	K562	blood:
8	chr19:51976397..51978354-chr19:51984183..51986699,2	K562	blood:
9	chr19:51975902..51976858-chr19:52110641..52111904,7	K562	blood:
10	chr19:51975931..51976838-chr19:52160089..52160663,2	MCF-7	breast:
11	chr19:51975869..51976891-chr19:52110720..52111476,3	MCF-7	breast:
12	chr19:51868665..51871642-chr19:51973620..51976713,3	K562	blood:
13	chr19:51976417..51978042-chr19:51981994..51984082,2	K562	blood:
14	chr19:51925342..51926122-chr19:51975926..51976809,2	K562	blood:
15	chr19:51976116..51976755-chr19:52018185..52018795,2	MCF-7	breast:

Variant related genes	Relation type
SIGLEC26P	TF binding region
CEACAM18	TF binding region
ENSG00000269403	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000105379	Chromatin interaction
ENSG00000160318	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10424482	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10424572	0.89[EUR][1000 genomes]
rs10424783	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10424804	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878257	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11878282	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11878388	0.89[EUR][1000 genomes]
rs11881105	0.80[EUR][1000 genomes]
rs16982729	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17206902	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs185254	0.86[EUR][1000 genomes]
rs2607257	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2607258	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2607259	0.87[EUR][1000 genomes]
rs2607260	0.86[EUR][1000 genomes]
rs28539101	0.87[EUR][1000 genomes]
rs28607420	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2864090	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2864091	0.87[EUR][1000 genomes]
rs2864092	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2864093	0.87[EUR][1000 genomes]
rs36503	0.86[EUR][1000 genomes]
rs56799568	0.89[EUR][1000 genomes]
rs61201251	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62115066	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62116369	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62116370	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62116371	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62116417	0.89[EUR][1000 genomes]
rs62116418	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62116420	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62116422	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7246811	0.89[EUR][1000 genomes]
rs8101777	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8107537	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51975000-51976600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr19:51975800-51981600	Enhancers	Fetal Intestine Small	intestine
3	chr19:51975800-51981800	Enhancers	Fetal Intestine Large	intestine
4	chr19:51976000-51976800	Weak transcription	Gastric	stomach
5	chr19:51976000-51977400	Genic enhancers	K562	blood
6	chr19:51976200-51976800	Enhancers	Stomach Mucosa	stomach
7	chr19:51976400-51976600	Enhancers	Primary hematopoietic stem cells	blood
8	chr19:51976400-51976800	Enhancers	Primary B cells from peripheral blood	blood
9	chr19:51976400-51976800	Active TSS	Duodenum Mucosa	Duodenum

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