Variant report

Variant	rs9822648
Chromosome Location	chr3:139899766-139899767
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11706003	0.86[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11713717	0.81[ASN][1000 genomes]
rs12629075	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35260142	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4305391	0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4336075	0.82[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4361242	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683810	0.82[CEU][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4683811	0.83[CHD][hapmap]
rs6767999	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612325	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810392	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9811727	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815878	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818249	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9818563	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818712	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823347	0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9825100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9856654	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs9876646	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv829739	chr3:139797496-140002685	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9822648	CHST2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139877000-139901200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:139890600-139901200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:139898600-139900200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:139898600-139900800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:139898800-139900000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:139898800-139901800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr3:139899000-139900000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:139899000-139900000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:139899000-139900000	Enhancers	Psoas Muscle	Psoas
10	chr3:139899000-139900000	Enhancers	HMEC	breast
11	chr3:139899000-139900000	Enhancers	NHDF-Ad	bronchial
12	chr3:139899000-139900000	Enhancers	NHEK	skin
13	chr3:139899200-139900000	Enhancers	Adipose Nuclei	Adipose
14	chr3:139899200-139904600	Weak transcription	HSMMtube	muscle
15	chr3:139899600-139900000	Enhancers	Esophagus	oesophagus

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