Variant report

Variant	rs10419607
Chromosome Location	chr19:42210659-42210660
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	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	REST	chr19:42210579-42210819	HepG2	liver:	n/a	chr19:42210720-42210729
3	YY1	chr19:42210567-42211073	A549	lung:	n/a	n/a
4	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
5	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
6	REST	chr19:42210516-42210964	ECC-1	luminal epithelium:	n/a	chr19:42210720-42210729
7	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
8	REST	chr19:42210627-42210836	Hela-S3	cervix:	n/a	chr19:42210720-42210729
9	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
10	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
11	REST	chr19:42210539-42211125	U87	brain:	n/a	chr19:42210720-42210729
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	CTCF	chr19:42210640-42210790	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
14	CTCF	chr19:42210640-42210790	HMF	breast:	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	chr19:42208811-42212212	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
16	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
17	REST	chr19:42210651-42210790	PANC-1	pancreas:	n/a	chr19:42210720-42210729
18	SMC3	chr19:42210560-42211126	Hela-S3	cervix:	n/a	chr19:42210744-42210758
19	EBF1	chr19:42210632-42210987	GM12878	blood:	n/a	chr19:42210781-42210792
20	MAZ	chr19:42210536-42210879	HepG2	liver:	n/a	chr19:42210655-42210671
21	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
22	RAD21	chr19:42210434-42211294	A549	lung:	n/a	chr19:42210748-42210758 chr19:42210743-42210762 chr19:42210747-42210756 chr19:42210748-42210760 chr19:42210746-42210759
23	REST	chr19:42210635-42210821	HepG2	liver:	n/a	chr19:42210720-42210729
24	CTCF	chr19:42210640-42210790	GM12870	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
25	NFYA	chr19:42210637-42211060	Hela-S3	cervix:	n/a	n/a
26	PAX5	chr19:42210657-42210982	GM12892	blood:	n/a	n/a
27	REST	chr19:42210429-42211253	MCF-7	breast:	n/a	chr19:42210720-42210729 chr19:42210493-42210506
28	RAD21	chr19:42210453-42211277	HCT-116	colon:	n/a	chr19:42210748-42210758 chr19:42210743-42210762 chr19:42210747-42210756 chr19:42210748-42210760 chr19:42210746-42210759
29	SMC3	chr19:42210634-42211041	HepG2	liver:	n/a	chr19:42210744-42210758
30	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
31	MAX	chr19:42210465-42211237	A549	lung:	n/a	chr19:42210655-42210671
32	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
33	CTCF	chr19:42210640-42210790	GM12869	blood:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
34	REST	chr19:42210491-42211093	MCF-7	breast:	n/a	chr19:42210720-42210729 chr19:42210493-42210506
35	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
36	YY1	chr19:42210636-42210981	GM12891	blood:	n/a	n/a
37	CTCFL	chr19:42210638-42210848	K562	blood:	n/a	chr19:42210749-42210758
38	CTCF	chr19:42210624-42211074	LNCaP	prostate:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
39	CTCF	chr19:42210640-42210790	HCPEpiC	choroid plexus:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
40	BCL3	chr19:42210325-42211072	A549	lung:	n/a	n/a
41	EGR1	chr19:42210649-42211120	K562	blood:	n/a	n/a
42	CTCF	chr19:42210566-42211260	HepG2	liver:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
43	REST	chr19:42210454-42211125	U87	brain:	n/a	chr19:42210720-42210729 chr19:42210493-42210506
44	CTCF	chr19:42210364-42211318	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
45	CTCF	chr19:42210581-42211158	GM12892	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	REST	chr19:42210565-42210927	PFSK-1	brain:	n/a	chr19:42210720-42210729
47	RAD21	chr19:42210586-42210799	Hela-S3	cervix:	n/a	chr19:42210748-42210758 chr19:42210743-42210762 chr19:42210747-42210756 chr19:42210748-42210760 chr19:42210746-42210759
48	MAX	chr19:42210330-42211317	A549	lung:	n/a	chr19:42210655-42210671
49	CTCF	chr19:42210608-42211127	Fibrobl	skin:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758
50	RAD21	chr19:42210585-42211080	H1-hESC	embryonic stem cell:	n/a	chr19:42210748-42210758 chr19:42210743-42210762 chr19:42210747-42210756 chr19:42210748-42210760 chr19:42210746-42210759

No.	Distal block	Cell Line	Cell type
1	chr19:42190379..42192601-chr19:42208251..42211218,2	K562	blood:
2	chr19:42210268..42210769-chr19:42257717..42258347,2	MCF-7	breast:
3	chr19:42206272..42207887-chr19:42208137..42210800,2	K562	blood:
4	chr19:42201688..42202322-chr19:42210240..42210766,2	K562	blood:

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

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10403227	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10406175	1.00[YRI][hapmap]
rs10406739	1.00[YRI][hapmap]
rs10408028	1.00[YRI][hapmap]
rs10409657	1.00[AFR][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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42203800-42210800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:42204800-42210800	Weak transcription	Esophagus	oesophagus
3	chr19:42206000-42210800	Weak transcription	Pancreas	Pancrea
4	chr19:42206600-42210800	Weak transcription	Placenta	Placenta
5	chr19:42210200-42211600	Bivalent Enhancer	Stomach Mucosa	stomach
6	chr19:42210600-42210800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr19:42210600-42210800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr19:42210600-42210800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr19:42210600-42210800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr19:42210600-42210800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:42210600-42210800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:42210600-42210800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:42210600-42210800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:42210600-42211000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr19:42210600-42211000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr19:42210600-42211000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:42210600-42211000	Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr19:42210600-42211000	Active TSS	Primary B cells from cord blood	blood
19	chr19:42210600-42211000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr19:42210600-42211000	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:42210600-42211000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:42210600-42211000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:42210600-42211000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
24	chr19:42210600-42211000	Flanking Active TSS	Fetal Intestine Small	intestine
25	chr19:42210600-42211000	Active TSS	Gastric	stomach
26	chr19:42210600-42211000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr19:42210600-42211000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
28	chr19:42210600-42211000	Active TSS	A549	lung
29	chr19:42210600-42211000	Active TSS	Hela-S3	cervix
30	chr19:42210600-42211000	Active TSS	HepG2	liver
31	chr19:42210600-42211000	Active TSS	Monocytes-CD14+_RO01746	blood
32	chr19:42210600-42211200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr19:42210600-42211200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr19:42210600-42211400	Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links