Variant report

Variant	rs2239369
Chromosome Location	chr19:19292405-19292406
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19292259-19292724	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:19292401-19292468	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:19292054-19293994	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr19:19292283-19292578	K562	blood:	n/a	n/a
5	POLR2A	chr19:19292239-19292785	HL-60	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19286456..19293705-chr19:19298673..19304955,13	K562	blood:
2	chr19:19291248..19293065-chr19:19301550..19303514,2	K562	blood:
3	chr19:19291680..19293828-chr19:19294510..19298396,4	K562	blood:
4	chr19:19291324..19295055-chr19:19301522..19304242,3	MCF-7	breast:

No data

Variant related genes	Relation type
MEF2BNB	TF binding region
ENSG00000254901	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000064490	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10417796	0.86[EUR][1000 genomes]
rs10418053	0.96[CEU][hapmap];0.84[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs1050544	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs10854008	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10854009	0.85[EUR][1000 genomes]
rs10854012	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669408	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11669860	0.86[EUR][1000 genomes]
rs11669861	0.87[EUR][1000 genomes]
rs12609573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12972894	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12974672	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12975096	0.80[EUR][1000 genomes]
rs12975253	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12975290	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12980269	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12980955	0.85[EUR][1000 genomes]
rs12981160	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1858846	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2238668	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2239370	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs2283623	0.85[EUR][1000 genomes]
rs2314035	0.86[EUR][1000 genomes]
rs35342977	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3787040	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4808185	0.85[EUR][1000 genomes]
rs539	0.94[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62135499	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71332145	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7250650	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7256811	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7260127	0.88[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72997174	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs741706	0.88[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8101388	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv933613	chr19:19291456-19312244	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2239369	C19orf50	cis	cerebellum	SCAN
rs2239369	ZNF682	cis	parietal	SCAN
rs2239369	C19orf50	cis	parietal	SCAN
rs2239369	PDE4C	cis	cerebellum	SCAN
rs2239369	RAB8A	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
2	chr19:19280800-19301600	Weak transcription	NHEK	skin
3	chr19:19281400-19300800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:19281600-19293000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:19281600-19297200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:19281600-19299400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:19281600-19300600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:19281600-19302000	Weak transcription	NH-A	brain
9	chr19:19281600-19302200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:19281800-19300000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:19281800-19301200	Weak transcription	Stomach Mucosa	stomach
12	chr19:19282000-19301600	Weak transcription	Fetal Heart	heart
13	chr19:19283400-19300600	Weak transcription	Psoas Muscle	Psoas
14	chr19:19283400-19301600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:19283400-19302000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:19283400-19302200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:19283600-19301800	Weak transcription	HSMMtube	muscle
18	chr19:19284200-19302000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:19285600-19301800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:19286000-19292800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:19286000-19301000	Weak transcription	HepG2	liver
22	chr19:19286000-19302000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:19286400-19294000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:19286600-19293600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:19286600-19293600	Strong transcription	Ovary	ovary
26	chr19:19286600-19293800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr19:19286600-19298200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:19286800-19293800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr19:19286800-19293800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr19:19286800-19293800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr19:19286800-19294000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:19286800-19294000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:19286800-19296600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr19:19287000-19293600	Strong transcription	Gastric	stomach
35	chr19:19287000-19293800	Strong transcription	Pancreas	Pancrea
36	chr19:19287000-19293800	Strong transcription	Thymus	Thymus
37	chr19:19287000-19294000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:19287000-19294400	Strong transcription	Primary T cells from cord blood	blood
39	chr19:19287200-19293400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr19:19287200-19293800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:19287200-19293800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:19287200-19293800	Strong transcription	Dnd41	blood
43	chr19:19287200-19294000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr19:19287200-19294000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:19287200-19294000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:19287400-19293600	Strong transcription	Colonic Mucosa	Colon
47	chr19:19287400-19293800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:19287400-19293800	Strong transcription	Brain Anterior Caudate	brain
49	chr19:19287400-19293800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr19:19287600-19293800	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links