Variant report

Variant	rs11083455
Chromosome Location	chr19:38876464-38876465
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38875977-38876597	A549	lung:	n/a	n/a
2	POLR2A	chr19:38874550-38877193	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:38876432-38876652	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr19:38874034-38876600	K562	blood:	n/a	n/a
5	POLR2A	chr19:38871440-38886227	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr19:38874152-38877033	GM12891	blood:	n/a	n/a
7	POLR2A	chr19:38876401-38876614	A549	lung:	n/a	n/a
8	POLR2A	chr19:38874785-38879102	A549	lung:	n/a	n/a
9	POLR2A	chr19:38874623-38876880	GM12891	blood:	n/a	n/a
10	POLR2A	chr19:38869603-38879135	K562	blood:	n/a	n/a
11	POLR2A	chr19:38874605-38876529	K562	blood:	n/a	n/a
12	POLR2A	chr19:38875923-38876669	A549	lung:	n/a	n/a
13	POLR2A	chr19:38873616-38876905	A549	lung:	n/a	n/a
14	POLR2A	chr19:38874705-38876483	HL-60	blood:	n/a	n/a
15	POLR2A	chr19:38876234-38876753	H1-hESC	embryonic stem cell:	n/a	n/a
16	EGR1	chr19:38876351-38876725	K562	blood:	n/a	n/a
17	POLR2A	chr19:38874471-38877088	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr19:38873453-38879163	K562	blood:	n/a	n/a
19	POLR2A	chr19:38874175-38877146	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:38873627-38879112	K562	blood:	n/a	n/a
21	POLR2A	chr19:38873798-38877126	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr19:38874901-38876812	GM19193	blood:	n/a	n/a
23	POLR2A	chr19:38874768-38876500	U87	brain:	n/a	n/a
24	POLR2A	chr19:38874068-38876982	GM12892	blood:	n/a	n/a
25	POLR2A	chr19:38874772-38877051	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:38876299-38876733	GM12878	blood:	n/a	n/a
27	CCNT2	chr19:38876270-38877985	K562	blood:	n/a	n/a
28	POLR2A	chr19:38874370-38877112	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:38873479-38877165	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:38873532-38876808	GM12892	blood:	n/a	n/a
31	POLR2A	chr19:38873689-38876797	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:38873576-38876991	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr19:38873583-38876671	K562	blood:	n/a	n/a
34	POLR2A	chr19:38876392-38876654	GM12892	blood:	n/a	n/a
35	POLR2A	chr19:38874801-38877095	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:38876175..38878484-chr19:38901904..38903905,2	K562	blood:
2	chr19:38873942..38878444-chr19:38892255..38895006,5	K562	blood:
3	chr19:36630602..36632414-chr19:38875371..38878496,3	MCF-7	breast:
4	chr19:38804471..38807313-chr19:38874109..38876554,2	MCF-7	breast:
5	chr19:38824957..38829265-chr19:38874295..38879043,8	MCF-7	breast:

No data

Variant related genes	Relation type
SPRED3	TF binding region
ENSG00000171777	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000130244	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12609878	0.82[AMR][1000 genomes]
rs61162240	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription 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	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	esv3361438	chr19:38875337-38877885	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38867000-38877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38867000-38878000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:38867200-38877000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:38867200-38877200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:38867200-38877400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:38867600-38877400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:38867800-38876600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:38867800-38877000	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr19:38868000-38877600	Weak transcription	Right Atrium	heart
10	chr19:38869600-38876600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:38869600-38877400	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:38869600-38877800	Strong transcription	NHLF	lung
13	chr19:38870200-38877400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:38870400-38876800	Strong transcription	Ovary	ovary
15	chr19:38873000-38877800	Weak transcription	Hela-S3	cervix
16	chr19:38873200-38877600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:38874000-38876600	Strong transcription	Esophagus	oesophagus
18	chr19:38874000-38877600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr19:38874400-38877600	Weak transcription	HUVEC	blood vessel
20	chr19:38874600-38876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:38874600-38877200	Weak transcription	NH-A	brain
22	chr19:38874600-38877800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:38874800-38876600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:38874800-38876800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:38874800-38876800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr19:38874800-38877000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:38874800-38877200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:38874800-38877200	Weak transcription	NHDF-Ad	bronchial
29	chr19:38874800-38878000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:38874800-38878000	Weak transcription	HepG2	liver
31	chr19:38874800-38878200	Weak transcription	HSMMtube	muscle
32	chr19:38875000-38876600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:38875000-38876600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr19:38875000-38876600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:38875000-38876800	Enhancers	H1 Cell Line	embryonic stem cell
36	chr19:38875000-38876800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:38875000-38877000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr19:38875000-38877200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:38875000-38877400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr19:38875000-38877800	Weak transcription	HSMM	muscle
41	chr19:38875000-38878000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:38875200-38876600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:38875200-38877200	Weak transcription	Left Ventricle	heart
44	chr19:38875200-38877600	Weak transcription	Liver	Liver
45	chr19:38875200-38877800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:38875200-38878400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:38875200-38878400	Weak transcription	Aorta	Aorta
48	chr19:38875400-38877600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:38875400-38877600	Weak transcription	Osteobl	bone
50	chr19:38875600-38877200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood

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