Variant report

Variant	rs9897434
Chromosome Location	chr17:20891402-20891403
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20889603..20892267-chr17:20894765..20897394,3	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1038109	0.91[JPT][hapmap]
rs1044410	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1044414	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1044420	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs11204328	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11650829	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11651632	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11654347	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11654680	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655364	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655562	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11658822	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11658914	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11659113	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11871167	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600604	0.93[ASN][1000 genomes]
rs12936249	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531567	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993901	0.86[JPT][hapmap]
rs2009756	0.86[JPT][hapmap]
rs2291036	0.87[JPT][hapmap]
rs2291037	0.91[JPT][hapmap]
rs2364328	0.82[JPT][hapmap]
rs2364332	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2364333	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs28419675	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28595150	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3612	0.91[JPT][hapmap]
rs3816664	0.91[JPT][hapmap]
rs3943299	0.91[JPT][hapmap]
rs4985813	0.82[ASN][1000 genomes]
rs4985820	0.87[JPT][hapmap]
rs4985935	0.91[JPT][hapmap]
rs4985941	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4985946	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985947	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985948	0.88[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs4985949	0.92[ASN][1000 genomes]
rs4985952	0.92[ASN][1000 genomes]
rs4985953	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4985954	0.85[ASN][1000 genomes]
rs4985955	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4985962	0.91[JPT][hapmap]
rs4985974	0.83[JPT][hapmap]
rs5005801	0.91[JPT][hapmap]
rs55730423	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55749232	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55985304	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62056767	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587109	0.91[JPT][hapmap]
rs6587115	0.87[JPT][hapmap]
rs6650606	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6650607	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7211094	0.86[JPT][hapmap]
rs7213253	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7215369	0.91[JPT][hapmap]
rs7216090	0.82[ASN][1000 genomes]
rs7219244	0.85[JPT][hapmap]
rs7220023	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7223388	0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7226229	0.86[JPT][hapmap]
rs8064435	0.95[JPT][hapmap]
rs8071311	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs8075790	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8076078	0.93[ASN][1000 genomes]
rs8082210	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880652	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs880654	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs899334	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs899335	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs899336	0.85[ASN][1000 genomes]
rs899338	0.85[ASN][1000 genomes]
rs899342	0.86[JPT][hapmap]
rs961004	0.93[ASN][1000 genomes]
rs9797279	0.91[JPT][hapmap]
rs9896259	0.87[JPT][hapmap]
rs9896301	0.91[JPT][hapmap]
rs9896416	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9898265	0.86[JPT][hapmap]
rs996065	0.87[JPT][hapmap]

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	nsv2006	chr17:20846763-20892730	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9897434	RP11-344E13.3	cis	Whole Blood	GTEx
rs9897434	RP11-344E13.3	cis	Thyroid	GTEx
rs9897434	RP11-344E13.3	cis	Artery Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20848200-20896600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:20874600-20896600	Weak transcription	Spleen	Spleen
3	chr17:20881400-20896200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr17:20885800-20892800	Weak transcription	HepG2	liver
5	chr17:20886800-20896400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr17:20887000-20896600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr17:20887200-20891800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr17:20887200-20896000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:20890000-20892000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:20890000-20892400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:20890400-20892800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr17:20891000-20891800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:20891000-20897400	Weak transcription	Gastric	stomach
14	chr17:20891400-20891600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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