Variant report

Variant	rs1808393
Chromosome Location	chr19:56148639-56148640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56146082-56149393	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:56146066-56155822	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr19:56145990-56148670	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr19:56145947-56149686	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:56146054-56148734	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:56146995-56149583	K562	blood:	n/a	n/a
7	POLR2A	chr19:56148175-56148721	K562	blood:	n/a	n/a
8	POLR2A	chr19:56148530-56149394	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:56145941-56148656	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:56145999-56149668	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:56146014-56148713	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr19:56146039-56148828	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:56109995..56114029-chr19:56145200..56149074,4	MCF-7	breast:
2	chr19:56135345..56138507-chr19:56147845..56151809,4	K562	blood:
3	chr19:55917719..55921194-chr19:56143842..56149725,7	K562	blood:
4	chr19:56134501..56137412-chr19:56145689..56149345,6	K562	blood:

No data

Variant related genes	Relation type
CCDC106	TF binding region
ZNF580	TF binding region
ZNF581	TF binding region
ENSG00000108106	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000171443	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2864434	0.95[ASN][1000 genomes]
rs310436	0.81[ASN][1000 genomes]
rs485152	0.95[ASN][1000 genomes]
rs504850	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs519856	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs579496	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs596075	0.93[ASN][1000 genomes]
rs643368	0.95[ASN][1000 genomes]
rs664684	0.84[ASN][1000 genomes]
rs7247677	0.83[ASN][1000 genomes]
rs7252055	0.93[ASN][1000 genomes]
rs889092	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
6	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1808393	ZNF580	cis	Artery Tibial	GTEx
rs1808393	ZNF580	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56147400-56149200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:56147400-56149200	Genic enhancers	Fetal Muscle Leg	muscle
3	chr19:56147400-56149800	Enhancers	Gastric	stomach
4	chr19:56147600-56149000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr19:56147600-56149000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr19:56147600-56149000	Enhancers	Fetal Muscle Trunk	muscle
7	chr19:56147600-56149200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:56147600-56149200	Enhancers	Primary B cells from cord blood	blood
9	chr19:56147600-56149200	Enhancers	Primary B cells from peripheral blood	blood
10	chr19:56147600-56149200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr19:56147600-56149200	Enhancers	Brain Germinal Matrix	brain
12	chr19:56147600-56149400	Enhancers	Ovary	ovary
13	chr19:56147600-56149400	Enhancers	Spleen	Spleen
14	chr19:56147600-56149600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:56147600-56150400	Weak transcription	Fetal Brain Female	brain
16	chr19:56147800-56149000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:56147800-56149400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:56147800-56149400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr19:56147800-56149400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr19:56147800-56149600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:56147800-56149600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:56147800-56150400	Strong transcription	Fetal Intestine Small	intestine
23	chr19:56147800-56151400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:56147800-56151400	Enhancers	Liver	Liver
25	chr19:56147800-56151400	Enhancers	Brain Substantia Nigra	brain
26	chr19:56147800-56151600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:56147800-56151600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:56147800-56151600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:56147800-56151600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr19:56147800-56151600	Weak transcription	Fetal Heart	heart
31	chr19:56147800-56151600	Enhancers	Pancreas	Pancrea
32	chr19:56147800-56151800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:56147800-56151800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr19:56148000-56148800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:56148000-56149000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:56148000-56149400	Weak transcription	Fetal Intestine Large	intestine
37	chr19:56148000-56149600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr19:56148000-56150400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:56148000-56150400	Weak transcription	Fetal Brain Male	brain
40	chr19:56148000-56150600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr19:56148000-56150800	Weak transcription	Fetal Kidney	kidney
42	chr19:56148000-56151400	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr19:56148200-56148800	Enhancers	Primary T cells from cord blood	blood
44	chr19:56148200-56149000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:56148200-56149200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr19:56148200-56149200	Enhancers	Colon Smooth Muscle	Colon
47	chr19:56148200-56149400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:56148200-56149400	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr19:56148200-56149400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:56148200-56149400	Enhancers	Brain Angular Gyrus	brain

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