Variant report

Variant	rs899
Chromosome Location	chr1:79003355-79003356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11162508	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060353	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069538	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074883	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[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];1.00[ASN][1000 genomes]
rs12723149	1.00[ASN][1000 genomes]
rs12731181	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[LWK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737007	1.00[ASN][1000 genomes]
rs12743477	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750516	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751216	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17393482	1.00[ASN][1000 genomes]
rs17397597	1.00[ASN][1000 genomes]
rs2057425	0.86[ASN][1000 genomes]
rs34427371	1.00[ASN][1000 genomes]
rs34491075	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34635429	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34727624	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35153996	0.85[EUR][1000 genomes]
rs35223399	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35337590	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35735651	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35886379	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35922757	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36037890	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36088152	1.00[ASN][1000 genomes]
rs41309153	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs41313355	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71641401	1.00[ASN][1000 genomes]
rs71643204	1.00[ASN][1000 genomes]
rs71643205	0.81[EUR][1000 genomes]
rs7539356	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539847	1.00[ASN][1000 genomes]
rs898	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[LWK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv870807	chr1:78867347-79032598	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv870919	chr1:78993841-79010670	Enhancers Strong transcription Weak transcription Genic enhancers	miRNA target site	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs899	TYW3	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79002600-79004000	Strong transcription	NHDF-Ad	bronchial
2	chr1:79002800-79003400	Weak transcription	Osteobl	bone
3	chr1:79002800-79004200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:79002800-79007200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:79003000-79005800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:79003200-79003600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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