Variant report

Variant	rs9823347
Chromosome Location	chr3:139894395-139894396
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11706003	0.87[CEU][hapmap];0.89[GIH][hapmap];0.80[ASN][1000 genomes]
rs11713717	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12629075	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4305391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4336075	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4361242	0.82[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4683810	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6767999	0.87[ASN][1000 genomes]
rs7612325	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9810392	0.87[CEU][hapmap];0.89[GIH][hapmap];0.80[ASN][1000 genomes]
rs9811727	0.87[ASN][1000 genomes]
rs9815878	0.87[ASN][1000 genomes]
rs9818249	0.84[ASN][1000 genomes]
rs9818563	0.87[ASN][1000 genomes]
rs9818712	0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9822648	0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9825100	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9876646	0.87[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
rs9823347	CHST2	cis	cerebellum	SCAN

Chromatin state (count:8 , 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	chr3:139885600-139899200	Weak transcription	Adipose Nuclei	Adipose
3	chr3:139886400-139895400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:139886600-139895200	Weak transcription	Ovary	ovary
5	chr3:139889600-139894800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:139890400-139894600	Weak transcription	HSMMtube	muscle
7	chr3:139890600-139901200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:139893800-139894600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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