Variant report

Variant	rs583315
Chromosome Location	chr1:86526618-86526619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10047143	0.82[EUR][1000 genomes]
rs10873744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11161713	0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11161734	0.89[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs12029694	0.85[EUR][1000 genomes]
rs12040977	0.84[CEU][hapmap]
rs12040981	0.84[CEU][hapmap]
rs12043664	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs12118004	0.84[EUR][1000 genomes]
rs12134342	0.84[EUR][1000 genomes]
rs17405097	0.86[ASW][hapmap];0.85[CHD][hapmap];0.83[LWK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs489385	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs498554	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516213	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs535637	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs551219	0.85[GIH][hapmap];0.85[MEX][hapmap]
rs569419	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs582141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585708	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs610639	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613060	0.86[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61802174	0.96[EUR][1000 genomes]
rs640303	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs648833	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs662369	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6672107	0.89[CEU][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs680613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537787	0.84[EUR][1000 genomes]
rs997110	0.96[CEU][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs9988602	0.82[EUR][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	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525678	chr1:86487914-86549498	Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs583315	LOC339524	cis	parietal	SCAN
rs583315	LOC339524	cis	cerebellum	SCAN
rs583315	COL24A1	cis	Artery Tibial	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86521000-86527200	Weak transcription	Fetal Lung	lung
2	chr1:86523000-86533800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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