Variant report

Variant	rs6487539
Chromosome Location	chr12:26342988-26342989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1009766	0.82[CHD][hapmap]
rs10842684	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1473431	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1480034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552041	0.94[ASW][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.96[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs16930287	0.90[ASN][1000 genomes]
rs16930293	0.85[JPT][hapmap]
rs1871554	0.83[ASN][1000 genomes]
rs1871555	0.90[ASN][1000 genomes]
rs56198343	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56713764	0.81[ASN][1000 genomes]
rs6487540	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73086956	0.83[ASN][1000 genomes]
rs73086959	0.83[ASN][1000 genomes]
rs7969850	0.81[CHD][hapmap]
rs7979281	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804706	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv648	chr12:26330291-26375186	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6487539	GUCY2D	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26338800-26348200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:26341000-26343000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:26341800-26348000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:26341800-26348000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:26341800-26348000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:26341800-26348000	Weak transcription	A549	lung
7	chr12:26341800-26348000	Weak transcription	NH-A	brain
8	chr12:26341800-26348000	Weak transcription	NHEK	skin
9	chr12:26341800-26348000	Weak transcription	Osteobl	bone

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