Variant report

Variant	rs2057425
Chromosome Location	chr1:79026487-79026488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11162508	0.86[ASN][1000 genomes]
rs12060353	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12065196	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs12069538	0.86[ASN][1000 genomes]
rs12074883	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs12723149	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12731181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12737007	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12743477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12750516	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12751216	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17393482	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17397597	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2146490	0.82[EUR][1000 genomes]
rs34427371	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34491075	0.86[ASN][1000 genomes]
rs34635429	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34727624	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35153996	0.94[EUR][1000 genomes]
rs35223399	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35337590	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35735651	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35886379	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35922757	0.86[ASN][1000 genomes]
rs36037890	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36088152	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41309153	0.94[EUR][1000 genomes]
rs41313355	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67458600	0.82[EUR][1000 genomes]
rs71641401	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71643204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71643205	0.93[EUR][1000 genomes]
rs7539356	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7539847	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs899	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[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	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	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	esv3375099	chr1:79010980-79033337	Enhancers Weak transcription ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
5	nsv1577	chr1:79013311-79058575	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2057425	TYW3	cis	cerebellum	SCAN
rs2057425	ST6GALNAC5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79026000-79028600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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