Variant report

Variant	rs11673394
Chromosome Location	chr19:42211307-42211308
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	chr19:42211280-42211430	HFF	foreskin:	n/a	n/a
2	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
3	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
4	CTCF	chr19:42211264-42211328	GM19238	blood:	n/a	n/a
5	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
6	MAX	chr19:42210330-42211317	A549	lung:	n/a	chr19:42210655-42210671
7	CTCF	chr19:42211200-42211350	HL-60	blood:	n/a	n/a
8	CTCF	chr19:42210208-42211748	HCT-116	colon:	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
9	CTCF	chr19:42211220-42211370	K562	blood:	n/a	n/a
10	REST	chr19:42208676-42211670	A549	lung:	n/a	chr19:42209562-42209582 chr19:42211482-42211495 chr19:42209563-42209581 chr19:42209569-42209582 chr19:42209564-42209572 chr19:42209566-42209579 chr19:42210720-42210729 chr19:42209562-42209582 chr19:42211402-42211415 chr19:42209562-42209576 chr19:42209573-42209582 chr19:42209568-42209577 chr19:42210493-42210506 chr19:42209689-42209702 chr19:42209562-42209582
11	CTCF	chr19:42210347-42211724	SK-N-SH	brain:	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
12	CTCF	chr19:42211246-42211312	GM10266	blood:	n/a	n/a
13	CTCF	chr19:42210396-42211390	HCT-116	colon:	n/a	chr19:42210745-42210754 chr19:42210744-42210765 chr19:42210743-42210759 chr19:42210747-42210757 chr19:42210742-42210760 chr19:42210745-42210758 chr19:42210745-42210758

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42211076..42212814-chr19:42288522..42291440,2	MCF-7	breast:

Variant related genes	Relation type
CEACAM7	TF binding region
CEACAM5	TF binding region
ENSG00000267881	TF binding region
ENSG00000268833	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1001578	0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs10403308	0.88[CHB][hapmap]
rs10406899	0.85[ASN][1000 genomes]
rs10415317	0.83[CHB][hapmap]
rs10415946	0.83[CHB][hapmap]
rs10417322	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10425443	0.83[CHB][hapmap]
rs11083637	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11878239	0.83[CHB][hapmap]
rs11878262	0.82[CHB][hapmap]
rs12971712	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12985771	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs1593086	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2002926	0.83[CHB][hapmap]
rs3764577	0.83[CHB][hapmap]
rs3764579	0.83[CHB][hapmap]
rs3928916	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4802127	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802129	0.83[CHB][hapmap]
rs4803503	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803506	0.83[CHB][hapmap]
rs7247317	0.90[ASN][1000 genomes]
rs7255070	0.83[CHB][hapmap]
rs748249	0.83[CHB][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11673394	SYMPK	cis	cerebellum	SCAN
rs11673394	ATF5	cis	parietal	SCAN
rs11673394	CCDC155	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42210200-42211600	Bivalent Enhancer	Stomach Mucosa	stomach
2	chr19:42210600-42211400	Active TSS	K562	blood
3	chr19:42210800-42211600	Enhancers	Fetal Intestine Large	intestine
4	chr19:42210800-42211800	Enhancers	Esophagus	oesophagus
5	chr19:42210800-42212000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:42210800-42212000	Enhancers	Spleen	Spleen
7	chr19:42210800-42212400	Flanking Active TSS	Colonic Mucosa	Colon
8	chr19:42211000-42211400	Enhancers	Fetal Intestine Small	intestine
9	chr19:42211000-42211400	Flanking Active TSS	A549	lung
10	chr19:42211000-42211600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:42211000-42212400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr19:42211000-42214200	Active TSS	Rectal Smooth Muscle	rectum
13	chr19:42211200-42211800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr19:42211200-42212000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
15	chr19:42211200-42212600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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