Variant report

Variant	rs9450273
Chromosome Location	chr6:86137888-86137889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10944128	0.81[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs10944129	0.88[ASN][1000 genomes]
rs11752251	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12191637	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12203963	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12213716	0.87[AMR][1000 genomes]
rs2842600	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2842611	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs4288177	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4431401	0.81[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs4706238	0.87[AMR][1000 genomes]
rs4707211	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6454472	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6927475	0.86[ASN][1000 genomes]
rs7766485	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs9444348	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444352	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs9450277	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450285	0.81[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9450288	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs9885944	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv830721	chr6:85987644-86147414	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs9450273	KIAA1009	cis	cerebellum	SCAN
rs9450273	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs9450273	SNHG5	cis	Artery Aorta	GTEx
rs9450273	NT5E	cis	Thyroid	GTEx
rs9450273	SNHG5	cis	Artery Tibial	GTEx
rs9450273	SNHG5	cis	Esophagus Mucosa	GTEx
rs9450273	SNHG5	cis	Whole Blood	GTEx
rs9450273	C6orf160	cis	multi-tissue	Pritchard
rs9450273	C6orf160	cis	uninvolved skin	skin_eQTL
rs9450273	C6orf160	cis	lesional skin	skin_eQTL
rs9450273	C6orf160	cis	normal skin	skin_eQTL
rs9450273	SNHG5	cis	Nerve Tibial	GTEx
rs9450273	SNHG5	cis	Esophagus Muscularis	GTEx
rs9450273	HSS00211180	cis	multi-tissue	Pritchard
rs9450273	SNHG5	cis	Adipose Subcutaneous	GTEx
rs9450273	SNHG5	cis	Muscle Skeletal	GTEx
rs9450273	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs9450273	SNHG5	cis	Heart Left Ventricle	GTEx
rs9450273	SNHG5	cis	lung	GTEx
rs9450273	SNHG5	cis	multi-tissue	Pritchard
rs9450273	SNHG5	cis	Thyroid	GTEx
rs9450273	SNHG5	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86129800-86157400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:86132400-86145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:86137600-86139600	Enhancers	NHDF-Ad	bronchial

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