Variant report

Variant	rs9896416
Chromosome Location	chr17:20876002-20876003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1044410	0.81[ASN][1000 genomes]
rs1044414	0.81[ASN][1000 genomes]
rs1044420	0.81[ASN][1000 genomes]
rs11204324	0.80[ASN][1000 genomes]
rs11204328	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650829	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651632	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654347	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11654680	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11655364	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11655562	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11658822	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11658914	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11659113	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11871167	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12600604	0.94[ASN][1000 genomes]
rs12936249	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1531567	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2009756	0.81[ASN][1000 genomes]
rs2364332	0.81[ASN][1000 genomes]
rs2364333	0.81[ASN][1000 genomes]
rs28419675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28595150	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985813	0.83[ASN][1000 genomes]
rs4985941	0.88[ASN][1000 genomes]
rs4985946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985947	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985948	0.94[ASN][1000 genomes]
rs4985949	0.93[ASN][1000 genomes]
rs4985952	0.93[ASN][1000 genomes]
rs4985953	0.86[ASN][1000 genomes]
rs4985954	0.86[ASN][1000 genomes]
rs4985955	0.86[ASN][1000 genomes]
rs55730423	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55749232	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55985304	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62056767	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6650606	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650607	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213253	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216090	0.83[ASN][1000 genomes]
rs7220023	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223388	0.91[ASN][1000 genomes]
rs8075790	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8076078	0.94[ASN][1000 genomes]
rs8082210	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs880652	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880654	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899334	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899335	0.86[ASN][1000 genomes]
rs899336	0.86[ASN][1000 genomes]
rs899338	0.86[ASN][1000 genomes]
rs961004	0.94[ASN][1000 genomes]
rs9797279	0.80[ASN][1000 genomes]
rs9897434	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1064365	chr17:20801739-20890716	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
rs9896416	RP11-344E13.3	cis	Whole Blood	GTEx
rs9896416	RP11-344E13.3	cis	Thyroid	GTEx
rs9896416	RP11-344E13.3	cis	Artery Tibial	GTEx

Chromatin state (count:16 , 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	chr17:20852800-20882600	Weak transcription	K562	blood
3	chr17:20859000-20881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:20862600-20890800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:20866000-20886600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:20866200-20876200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr17:20868000-20884800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:20869600-20880400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr17:20870000-20883000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:20870600-20880400	Weak transcription	HepG2	liver
11	chr17:20871800-20886800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr17:20873200-20886400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr17:20873200-20890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr17:20874600-20878800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:20874600-20896600	Weak transcription	Spleen	Spleen
16	chr17:20875400-20881000	Weak transcription	Primary B cells from peripheral blood	blood

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