Variant report

Variant	rs899340
Chromosome Location	chr17:20912848-20912849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:20912607-20912885	K562	blood:	n/a	n/a
2	POLR2A	chr17:20912616-20912950	GM12891	blood:	n/a	n/a
3	POLR2A	chr17:20912658-20912898	GM12878	blood:	n/a	n/a
4	POLR2A	chr17:20912418-20912933	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr17:20910057-20917039	K562	blood:	n/a	n/a
6	POLR2A	chr17:20912448-20913124	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr17:20912411-20913034	GM12892	blood:	n/a	n/a
8	POLR2A	chr17:20912316-20913977	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr17:20912682-20913269	HepG2	liver:	n/a	n/a
10	POLR2A	chr17:20912733-20912856	GM12878	blood:	n/a	n/a
11	POLR2A	chr17:20912683-20912890	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr17:20912471-20913053	HepG2	liver:	n/a	n/a
13	POLR2A	chr17:20912400-20912899	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:20906821..20909810-chr17:20910174..20912861,2	MCF-7	breast:
2	chr17:20910993..20913376-chr17:20944825..20947091,2	K562	blood:
3	chr17:20910306..20913499-chr17:20915103..20918018,3	MCF-7	breast:

No data

Variant related genes	Relation type
USP22	TF binding region
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1045162	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1127814	0.89[ASN][1000 genomes]
rs12600703	0.89[JPT][hapmap]
rs12602058	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12943067	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12946114	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1531566	0.87[ASN][1000 genomes]
rs17770614	0.84[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2054464	0.89[ASN][1000 genomes]
rs2127095	0.89[ASN][1000 genomes]
rs2291034	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2364326	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4445951	0.91[ASN][1000 genomes]
rs4985814	0.89[ASN][1000 genomes]
rs4985815	0.87[ASN][1000 genomes]
rs4985816	0.89[ASN][1000 genomes]
rs4985959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985966	0.80[ASN][1000 genomes]
rs4985967	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985968	0.85[ASN][1000 genomes]
rs4985969	0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4985970	0.85[ASN][1000 genomes]
rs4985971	0.85[ASN][1000 genomes]
rs56323013	0.89[ASN][1000 genomes]
rs58235085	0.85[ASN][1000 genomes]
rs59543297	0.88[ASN][1000 genomes]
rs59713572	0.85[ASN][1000 genomes]
rs6587111	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6587114	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6618	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs719093	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7209129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216921	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9911289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs899340	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs899340	RP11-344E13.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20900200-20924000	Strong transcription	Fetal Stomach	stomach
2	chr17:20900600-20932400	Strong transcription	Fetal Intestine Small	intestine
3	chr17:20900800-20925600	Strong transcription	Fetal Brain Female	brain
4	chr17:20900800-20932200	Strong transcription	Brain Germinal Matrix	brain
5	chr17:20901400-20925200	Strong transcription	Fetal Lung	lung
6	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
7	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:20901800-20929400	Strong transcription	GM12878-XiMat	blood
9	chr17:20901800-20932000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:20901800-20932000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr17:20901800-20932400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:20902000-20925200	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr17:20902000-20932600	Strong transcription	Fetal Intestine Large	intestine
15	chr17:20902000-20935400	Strong transcription	Dnd41	blood
16	chr17:20902200-20918600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr17:20902200-20925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:20902200-20932400	Strong transcription	Fetal Thymus	thymus
19	chr17:20902200-20932600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr17:20902400-20927000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr17:20902400-20931600	Strong transcription	HMEC	breast
22	chr17:20902400-20932200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr17:20902400-20932200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr17:20902400-20932600	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr17:20902600-20924200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr17:20902600-20925400	Strong transcription	NHEK	skin
27	chr17:20902600-20932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:20902600-20932200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr17:20902600-20932400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr17:20902600-20932800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr17:20902800-20923600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:20902800-20925200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr17:20902800-20925200	Strong transcription	Colonic Mucosa	Colon
34	chr17:20903200-20917000	Strong transcription	Esophagus	oesophagus
35	chr17:20903200-20925200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr17:20903200-20932000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr17:20903400-20932000	Strong transcription	Liver	Liver
38	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr17:20903800-20924000	Strong transcription	Lung	lung
41	chr17:20903800-20925000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr17:20904000-20928200	Strong transcription	A549	lung
43	chr17:20904000-20931600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:20904200-20926600	Strong transcription	Primary T cells from cord blood	blood
45	chr17:20904600-20925200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr17:20904600-20925200	Strong transcription	NH-A	brain
47	chr17:20904800-20915000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:20904800-20924800	Strong transcription	Fetal Kidney	kidney
49	chr17:20905000-20923800	Strong transcription	Pancreas	Pancrea
50	chr17:20905000-20925200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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