Variant report

Variant	rs12705859
Chromosome Location	chr7:78586678-78586679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10226001	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs10277798	1.00[CEU][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12536821	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs12537792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12537793	0.91[CEU][hapmap];0.84[TSI][hapmap]
rs12539532	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs12705860	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1624161	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1642888	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs17505	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2052403	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2098180	0.86[CEU][hapmap]
rs2159687	0.83[CEU][hapmap];0.82[LWK][hapmap];0.82[TSI][hapmap]
rs4507689	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4727794	0.82[CEU][hapmap]
rs4727796	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs4730569	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4730597	0.83[CEU][hapmap]
rs4730619	0.86[CEU][hapmap]
rs5004248	0.83[CEU][hapmap]
rs6945664	0.82[LWK][hapmap]
rs6964007	0.95[CEU][hapmap]
rs763593	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs7792974	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs7797351	0.86[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap];0.90[ASN][1000 genomes]
rs7799287	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs984312	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs987435	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs987436	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv482826	chr7:78548319-78717605	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv471642	chr7:78548320-78717605	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12705859	GNAI1	cis	parietal	SCAN
rs12705859	PCLO	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78583200-78588200	Weak transcription	Osteobl	bone
2	chr7:78584000-78588200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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