Variant report

Variant	rs7258524
Chromosome Location	chr19:42210824-42210825
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	chr19:42210525-42211142	A549	lung:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
2	YY1	chr19:42210567-42211073	A549	lung:	n/a	n/a
3	CTCF	chr19:42210399-42211842	MCF-7	breast:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42211587-42211596 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42211584-42211602 chr19:42210745-42210758 chr19:42210745-42210758
4	CTCF	chr19:42210351-42211270	K562	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
5	REST	chr19:42210516-42210964	ECC-1	luminal epithelium:	n/a	chr19:42210720-42210729
6	CTCF	chr19:42210582-42211155	Gliobla	brain:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
7	REST	chr19:42210627-42210836	Hela-S3	cervix:	n/a	chr19:42210720-42210729
8	CTCF	chr19:42210590-42211160	K562	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
9	CTCF	chr19:42210549-42211116	ECC-1	luminal epithelium:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
10	REST	chr19:42210539-42211125	U87	brain:	n/a	chr19:42210720-42210729
11	CTCF	chr19:42210680-42210830	HVMF	connective:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
12	RAD21	chr19:42210651-42210954	HepG2	liver:	n/a	chr19:42210748-42210758 chr19:42210743-42210762 chr19:42210747-42210756 chr19:42210748-42210760 chr19:42210746-42210759
13	EBF1	chr19:42210665-42210988	GM12878	blood:	n/a	chr19:42210781-42210792
14	CTCF	chr19:42210680-42210830	SAEC	small airway:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
15	CTCF	chr19:42210700-42210850	HAc	cerebellar:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
16	MAX	chr19:42210799-42210983	K562	blood:	n/a	n/a
17	CTCF	chr19:42210760-42210910	BJ	skin:	n/a	n/a
18	CTCF	chr19:42210720-42210870	Hela-S3	cervix:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
19	CTCF	chr19:42208811-42212212	A549	lung:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42211587-42211596 chr19:42210743-42210759 chr19:42209068-42209076 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42211584-42211602 chr19:42210745-42210758 chr19:42210745-42210758
20	CTCF	chr19:42210680-42210830	GM12875	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
21	CTCF	chr19:42210680-42210830	Caco-2	colon:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
22	CTCF	chr19:42210651-42211090	GM13976	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
23	STAT5A	chr19:42210756-42210968	GM12878	blood:	n/a	chr19:42210816-42210827
24	SMC3	chr19:42210560-42211126	Hela-S3	cervix:	n/a	chr19:42210744-42210758
25	EBF1	chr19:42210632-42210987	GM12878	blood:	n/a	chr19:42210781-42210792
26	MAZ	chr19:42210536-42210879	HepG2	liver:	n/a	chr19:42210655-42210671
27	JUND	chr19:42210746-42211021	HepG2	liver:	n/a	n/a
28	CTCF	chr19:42210540-42211200	K562	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
29	CTCF	chr19:42210680-42210830	NHEK	skin:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
30	RAD21	chr19:42210434-42211294	A549	lung:	n/a	chr19:42210748-42210758 chr19:42210743-42210762 chr19:42210747-42210756 chr19:42210748-42210760 chr19:42210746-42210759
31	CTCF	chr19:42210680-42210830	GM06990	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
32	CTCF	chr19:42210720-42210870	GM12874	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
33	NFYA	chr19:42210637-42211060	Hela-S3	cervix:	n/a	n/a
34	PAX5	chr19:42210657-42210982	GM12892	blood:	n/a	n/a
35	REST	chr19:42210429-42211253	MCF-7	breast:	n/a	chr19:42210720-42210729 chr19:42210493-42210506
36	HMGN3	chr19:42210729-42211082	K562	blood:	n/a	n/a
37	CTCF	chr19:42210720-42210870	GM12875	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
38	RAD21	chr19:42210453-42211277	HCT-116	colon:	n/a	chr19:42210748-42210758 chr19:42210743-42210762 chr19:42210747-42210756 chr19:42210748-42210760 chr19:42210746-42210759
39	MAZ	chr19:42210763-42211066	GM12878	blood:	n/a	n/a
40	SMC3	chr19:42210634-42211041	HepG2	liver:	n/a	chr19:42210744-42210758
41	CTCF	chr19:42210625-42211110	Lung_OC	lung:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
42	CTCF	chr19:42210680-42210830	HCM	heart:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
43	MAX	chr19:42210465-42211237	A549	lung:	n/a	chr19:42210655-42210671
44	HCFC1	chr19:42210679-42210879	K562	blood:	n/a	n/a
45	CTCF	chr19:42210554-42211179	GM12878	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
46	PAX5	chr19:42210697-42210854	GM12878	blood:	n/a	n/a
47	REST	chr19:42210491-42211093	MCF-7	breast:	n/a	chr19:42210720-42210729 chr19:42210493-42210506
48	CTCF	chr19:42210594-42211145	A549	lung:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
49	CTCF	chr19:42210760-42210910	GM12878	blood:	n/a	n/a
50	ATF3	chr19:42210716-42211031	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42190379..42192601-chr19:42208251..42211218,2	K562	blood:

Variant related genes	Relation type
ENSG00000267881	TF binding region
CEACAM5	TF binding region
ENSG00000007306	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10402825	0.82[EUR][1000 genomes]
rs10415940	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12461373	0.85[EUR][1000 genomes]
rs12971352	0.80[EUR][1000 genomes]
rs12979109	0.85[EUR][1000 genomes]
rs28683503	0.80[EUR][1000 genomes]
rs34155934	0.82[AMR][1000 genomes]
rs35091611	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3928915	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3928918	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3928919	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7250222	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7256221	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs7256597	0.89[EUR][1000 genomes]
rs7257798	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs7257962	0.89[EUR][1000 genomes]
rs7259215	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73545183	0.84[AFR][1000 genomes]
rs889365	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3319146	chr19:42082639-42212929	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3319147	chr19:42082742-42212770	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3422975	chr19:42106166-42212774	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	nsv1061309	chr19:42187716-42228445	Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42210200-42211600	Bivalent Enhancer	Stomach Mucosa	stomach
2	chr19:42210600-42211000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr19:42210600-42211000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:42210600-42211000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:42210600-42211000	Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr19:42210600-42211000	Active TSS	Primary B cells from cord blood	blood
7	chr19:42210600-42211000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr19:42210600-42211000	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:42210600-42211000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:42210600-42211000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:42210600-42211000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
12	chr19:42210600-42211000	Flanking Active TSS	Fetal Intestine Small	intestine
13	chr19:42210600-42211000	Active TSS	Gastric	stomach
14	chr19:42210600-42211000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr19:42210600-42211000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
16	chr19:42210600-42211000	Active TSS	A549	lung
17	chr19:42210600-42211000	Active TSS	Hela-S3	cervix
18	chr19:42210600-42211000	Active TSS	HepG2	liver
19	chr19:42210600-42211000	Active TSS	Monocytes-CD14+_RO01746	blood
20	chr19:42210600-42211200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr19:42210600-42211200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr19:42210600-42211400	Active TSS	K562	blood
23	chr19:42210800-42211000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr19:42210800-42211000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
25	chr19:42210800-42211000	Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr19:42210800-42211000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr19:42210800-42211000	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
28	chr19:42210800-42211000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr19:42210800-42211000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:42210800-42211000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:42210800-42211000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:42210800-42211000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:42210800-42211000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:42210800-42211000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:42210800-42211000	Flanking Active TSS	Liver	Liver
36	chr19:42210800-42211000	Bivalent Enhancer	Brain Germinal Matrix	brain
37	chr19:42210800-42211000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr19:42210800-42211000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr19:42210800-42211000	Bivalent Enhancer	Right Ventricle	heart
40	chr19:42210800-42211000	Flanking Active TSS	Thymus	Thymus
41	chr19:42210800-42211000	Flanking Active TSS	HMEC	breast
42	chr19:42210800-42211200	Enhancers	Placenta	Placenta
43	chr19:42210800-42211200	Enhancers	Pancreas	Pancrea
44	chr19:42210800-42211600	Enhancers	Fetal Intestine Large	intestine
45	chr19:42210800-42211800	Enhancers	Esophagus	oesophagus
46	chr19:42210800-42212000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:42210800-42212000	Enhancers	Spleen	Spleen
48	chr19:42210800-42212400	Flanking Active TSS	Colonic Mucosa	Colon

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