Variant report

Variant	rs9294380
Chromosome Location	chr6:88152667-88152668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13214153	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103764	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2207144	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207146	0.86[ASN][1000 genomes]
rs2268993	0.85[ASN][1000 genomes]
rs2268994	0.85[ASN][1000 genomes]
rs2273129	0.86[ASN][1000 genomes]
rs2284908	0.81[ASN][1000 genomes]
rs6454630	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6905947	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6912958	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914299	1.00[CEU][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933587	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7761814	0.83[ASN][1000 genomes]
rs9294379	0.96[CEU][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294381	1.00[CEU][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444504	0.86[ASN][1000 genomes]
rs9444519	0.82[CEU][hapmap]
rs9450688	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450701	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450704	0.86[ASN][1000 genomes]
rs9450712	0.81[ASN][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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv965744	chr6:88151722-88154668	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9294380	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx
rs9294380	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs9294380	C6orf164	cis	Thyroid	GTEx
rs9294380	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9294380	C6orf164	cis	Whole Blood	GTEx
rs9294380	SLC35A1	cis	multi-tissue	Pritchard
rs9294380	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs9294380	C6orf164	cis	lung	GTEx
rs9294380	C6orf164	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88150000-88154400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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