Variant report

Variant	rs62116418
Chromosome Location	chr19:51976433-51976434
allele	A/G
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	chr19:51976320-51976470	HMEC	breast:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
2	CTCF	chr19:51976207-51976521	ECC-1	luminal epithelium:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
3	CTCF	chr19:51976231-51976467	SK-N-SH_RA	brain:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
4	CTCF	chr19:51976320-51976470	HVMF	connective:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
5	EP300	chr19:51976198-51976677	K562	blood:	n/a	n/a
6	CTCF	chr19:51976300-51976450	AG04449	skin:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
7	RAD21	chr19:51976235-51976532	K562	blood:	n/a	chr19:51976362-51976381
8	RAD21	chr19:51976038-51976770	HCT-116	colon:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
9	CTCF	chr19:51976320-51976470	MCF-7	breast:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
10	CTCF	chr19:51976216-51976533	GM12878	blood:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
11	CTCF	chr19:51976223-51976499	LNCaP	prostate:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
12	CTCF	chr19:51976320-51976470	K562	blood:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
13	POLR2A	chr19:51976159-51977200	K562	blood:	n/a	n/a
14	RAD21	chr19:51976141-51976596	MCF-7	breast:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
15	SMC3	chr19:51976172-51976564	Hela-S3	cervix:	n/a	chr19:51976363-51976377 chr19:51976363-51976371
16	CTCF	chr19:51976154-51976528	T-47D	breast:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
17	ZNF143	chr19:51976206-51976547	K562	blood:	n/a	n/a
18	CTCF	chr19:51976241-51976492	ECC-1	luminal epithelium:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
19	RAD21	chr19:51976103-51976485	H1-hESC	embryonic stem cell:	n/a	chr19:51976362-51976381
20	RAD21	chr19:51976174-51976585	IMR90	lung:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
21	RAD21	chr19:51976137-51976615	A549	lung:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
22	HCFC1	chr19:51976280-51976519	K562	blood:	n/a	n/a
23	CTCF	chr19:51976300-51976450	GM12873	blood:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
24	CTCF	chr19:51976225-51976495	GM12891	blood:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
25	RAD21	chr19:51976180-51976558	HepG2	liver:	n/a	chr19:51976362-51976381
26	CTCF	chr19:51976300-51976450	HUVEC	blood vessel:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
27	CTCF	chr19:51976300-51976450	HCPEpiC	choroid plexus:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
28	CTCF	chr19:51976320-51976470	NHLF	lung:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
29	RAD21	chr19:51976141-51976625	MCF-7	breast:	n/a	chr19:51976560-51976579 chr19:51976362-51976381
30	ARID3A	chr19:51976233-51976587	K562	blood:	n/a	n/a
31	JUND	chr19:51976204-51976541	K562	blood:	n/a	chr19:51976264-51976273
32	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
33	CTCF	chr19:51976240-51976500	Kidney_OC	kidney:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
34	RAD21	chr19:51976221-51976572	SK-N-SH_RA	brain:	n/a	chr19:51976362-51976381
35	CTCF	chr19:51976320-51976470	NHEK	skin:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
36	ZNF384	chr19:51976278-51976514	K562	blood:	n/a	n/a
37	CTCF	chr19:51976320-51976470	HCM	heart:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
38	CTCF	chr19:51976300-51976450	HMF	breast:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
39	CTCF	chr19:51976192-51976524	K562	blood:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
40	CTCF	chr19:51976320-51976470	AG10803	skin:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
41	CTCF	chr19:51976231-51976489	MCF-7	breast:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
42	CTCF	chr19:51976300-51976450	HPAF	blood vessel:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
43	CTCF	chr19:51976236-51976519	Pancreas_OC	pancreas:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
44	IRF1	chr19:51975954-51976586	K562	blood:	n/a	n/a
45	CTCF	chr19:51976320-51976470	A549	lung:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
46	CTCF	chr19:51976300-51976450	GM12878	blood:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
47	CTCF	chr19:51976230-51976503	K562	blood:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
48	CTCF	chr19:51976320-51976470	GM06990	blood:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
49	CTCF	chr19:51976218-51976514	HUVEC	blood vessel:	n/a	chr19:51976363-51976384 chr19:51976366-51976376 chr19:51976364-51976373 chr19:51976362-51976378 chr19:51976361-51976379 chr19:51976364-51976377
50	RAD21	chr19:51976254-51976483	K562	blood:	n/a	chr19:51976362-51976381

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	chr19:51974505..51976487-chr19:52010911..52013199,2	K562	blood:
8	chr19:51975813..51976889-chr19:52140105..52142089,6	K562	blood:
9	chr19:51976397..51978354-chr19:51984183..51986699,2	K562	blood:
10	chr19:51975902..51976858-chr19:52110641..52111904,7	K562	blood:
11	chr19:51975931..51976838-chr19:52160089..52160663,2	MCF-7	breast:
12	chr19:51975869..51976891-chr19:52110720..52111476,3	MCF-7	breast:
13	chr19:51868665..51871642-chr19:51973620..51976713,3	K562	blood:
14	chr19:51976417..51978042-chr19:51981994..51984082,2	K562	blood:
15	chr19:51925342..51926122-chr19:51975926..51976809,2	K562	blood:
16	chr19:51976116..51976755-chr19:52018185..52018795,2	MCF-7	breast:

Variant related genes	Relation type
CEACAM18	TF binding region
SIGLEC26P	TF binding region
ENSG00000269580	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000105379	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10424482	1.00[EUR][1000 genomes]
rs10424572	0.89[EUR][1000 genomes]
rs10424783	1.00[EUR][1000 genomes]
rs10424804	1.00[EUR][1000 genomes]
rs11878257	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11878282	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11878388	0.89[EUR][1000 genomes]
rs11881105	0.80[EUR][1000 genomes]
rs16982729	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16982732	0.88[ASN][1000 genomes]
rs17206902	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs185254	0.86[EUR][1000 genomes]
rs2607257	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2607258	0.87[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	1.00[EUR][1000 genomes]
rs2864090	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2864091	0.87[EUR][1000 genomes]
rs2864092	0.87[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	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62115066	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62116369	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62116370	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62116371	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62116417	0.89[EUR][1000 genomes]
rs62116419	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62116420	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62116422	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7246811	0.89[EUR][1000 genomes]
rs8101777	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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