Variant report

Variant	rs12731181
Chromosome Location	chr1:79002589-79002590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11162508	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060353	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065196	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[LWK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069538	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074883	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[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]
rs12723149	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737007	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750516	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751216	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17393482	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397597	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057425	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34427371	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34491075	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34635429	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34727624	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35153996	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35223399	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35337590	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35735651	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35886379	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35922757	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36037890	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36088152	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41309153	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41313355	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71641401	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71643204	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71643205	0.95[EUR][1000 genomes]
rs7539356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539847	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12731181	ST6GALNAC5	cis	parietal	SCAN
rs12731181	LRRC31	trans	lymphoblastoid	seeQTL
rs12731181	TYW3	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79000600-79003000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:79001000-79002600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:79001800-79003000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:79002000-79002600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:79002000-79002800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:79002200-79002800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:79002400-79002600	Genic enhancers	NHDF-Ad	bronchial
8	chr1:79002400-79002800	Enhancers	Osteobl	bone

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