Variant report

Variant	rs10055721
Chromosome Location	chr5:178166903-178166904
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10038176	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10040079	0.84[EUR][1000 genomes]
rs10043919	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10044496	0.86[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10479505	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249565	0.96[ASN][1000 genomes]
rs11747569	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11949789	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13173933	0.82[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs28438427	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4296820	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398651	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6859031	0.82[CEU][hapmap]
rs6860052	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6871083	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6873580	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887719	0.87[ASN][1000 genomes]
rs6888253	0.87[ASN][1000 genomes]
rs7715687	0.80[EUR][1000 genomes]
rs7716636	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7727396	0.87[ASN][1000 genomes]
rs7737159	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9329050	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv883217	chr5:178099758-178193081	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1031206	chr5:178149292-178283614	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537973	chr5:178149292-178283614	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10055721	HK3	cis	cerebellum	SCAN
rs10055721	ZNF879	cis	cerebellum	SCAN
rs10055721	OR2Y1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178165600-178170400	Enhancers	Adipose Nuclei	Adipose
2	chr5:178166000-178168000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:178166600-178168200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:178166600-178169000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr5:178166600-178224000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:178166800-178167200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:178166800-178167200	Enhancers	Esophagus	oesophagus
8	chr5:178166800-178168400	Enhancers	Placenta	Placenta
9	chr5:178166800-178169200	Enhancers	Placenta Amnion	Placenta Amnion

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