Variant report

Variant	rs7159947
Chromosome Location	chr14:20809491-20809492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RPC155	chr14:20809086-20809650	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:20806952..20809661-chr17:57921243..57922941,2	MCF-7	breast:
2	chr14:20808367..20810653-chr14:20924028..20926387,4	K562	blood:
3	chr14:20774140..20775643-chr14:20808067..20810191,2	K562	blood:
4	chr14:20809095..20813799-chr14:21074403..21078570,5	MCF-7	breast:
5	chr14:20807684..20813516-chr14:20919958..20928823,14	K562	blood:
6	chr14:20792687..20795168-chr14:20809070..20811262,2	K562	blood:
7	chr14:20808270..20815666-chr14:20919802..20926735,19	MCF-7	breast:
8	chr14:20809378..20813101-chr14:20879937..20884504,11	MCF-7	breast:

No data

Variant related genes	Relation type
PARP2	TF binding region
ENSG00000200225	Chromatin interaction
ENSG00000238344	Chromatin interaction
ENSG00000136319	Chromatin interaction
ENSG00000092094	Chromatin interaction
ENSG00000173464	Chromatin interaction
ENSG00000165782	Chromatin interaction
ENSG00000129566	Chromatin interaction
ENSG00000100823	Chromatin interaction
ENSG00000259060	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10148359	0.85[MEX][hapmap]
rs1132644	0.88[LWK][hapmap]
rs11623831	0.83[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12889262	0.88[LWK][hapmap]
rs1713411	0.88[YRI][hapmap]
rs1713413	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1713414	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1713415	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1713430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1760912	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1760918	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1760919	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1760921	0.90[YRI][hapmap]
rs1760923	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1889363	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1953224	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297616	0.85[MEX][hapmap]
rs2297617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2319190	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2678682	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2678683	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28410239	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28436942	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3093870	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3093890	0.85[MEX][hapmap]
rs3093900	0.82[EUR][1000 genomes]
rs3093907	0.84[CEU][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs3093909	0.82[EUR][1000 genomes]
rs3093939	0.85[MEX][hapmap]
rs3784244	0.91[LWK][hapmap]
rs4981158	0.85[MEX][hapmap]
rs4981975	0.86[AFR][1000 genomes]
rs6575168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7160770	0.85[ASW][hapmap];0.87[LWK][hapmap];0.86[AFR][1000 genomes]
rs878157	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
4	nsv541974	chr14:20517485-20901811	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
5	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv534131	chr14:20757405-20886235	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1042025	chr14:20787961-20817851	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
8	esv21015	chr14:20800765-21257878	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7159947	CCNB1IP1	cis	cerebellum	SCAN
rs7159947	TTC5	cis	cerebellum	SCAN
rs7159947	RPPH1	cis	parietal	SCAN
rs7159947	PARP2	cis	parietal	SCAN
rs7159947	PRMT5	cis	parietal	SCAN
rs7159947	RPPH1	cis	multi-tissue	Pritchard
rs7159947	CCNB1IP1	cis	parietal	SCAN
rs7159947	PARP2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20802000-20809600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr14:20802000-20810400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr14:20802400-20810400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr14:20803800-20809600	Weak transcription	HepG2	liver
5	chr14:20808000-20809600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr14:20809000-20809600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr14:20809400-20809600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr14:20809400-20809600	Weak transcription	K562	blood
9	chr14:20809400-20809800	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links