Variant report

Variant	rs17428564
Chromosome Location	chr4:95755436-95755437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10488912	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11097447	0.85[CEU][hapmap]
rs11939949	0.85[CEU][hapmap]
rs11944292	1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs12504235	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12508959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12510047	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12511896	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12511962	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12512031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12512679	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12512684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12512864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1348606	0.85[CEU][hapmap]
rs17401285	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17428494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17428501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17428550	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17428585	0.93[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17428830	1.00[CEU][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs17429175	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17500351	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17500448	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17500892	1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs17500926	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17501107	1.00[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2023836	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs28604506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2865409	0.82[EUR][1000 genomes]
rs2865411	1.00[CEU][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4446318	0.84[EUR][1000 genomes]
rs4623010	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs58645352	0.85[EUR][1000 genomes]
rs6835267	0.83[EUR][1000 genomes]
rs7698964	0.85[CEU][hapmap]
rs7699554	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs916875	1.00[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking 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	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv518579	chr4:95706337-95755544	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv594906	chr4:95713679-95755544	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1007391	chr4:95713679-95763860	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1002004	chr4:95717063-95755436	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv999588	chr4:95717063-95763860	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv997960	chr4:95719585-95766067	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv537188	chr4:95719585-95766067	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17428564	TSPAN5	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95750800-95764400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:95754200-95755600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr4:95755400-95755600	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr4:95755400-95755800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:95755400-95756000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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