Variant report

Variant	rs9831287
Chromosome Location	chr3:160579248-160579249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12494732	0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13080397	0.94[ASW][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.82[LWK][hapmap];0.96[YRI][hapmap]
rs1839017	0.94[ASW][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1839019	0.87[ASN][1000 genomes]
rs4256178	0.83[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap]
rs6799058	0.80[YRI][hapmap]
rs9809208	0.90[CHD][hapmap]
rs9810290	0.90[CHD][hapmap];0.87[ASN][1000 genomes]
rs9869116	0.83[ASW][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv32963	chr3:160555238-160603116	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9831287	PPM1L	cis	cerebellum	SCAN
rs9831287	IFT80	cis	parietal	SCAN
rs9831287	GFM1	cis	parietal	SCAN
rs9831287	TRIM59	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160569600-160587800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:160577000-160579600	Weak transcription	Psoas Muscle	Psoas
3	chr3:160578400-160580000	Enhancers	Thymus	Thymus
4	chr3:160578400-160584400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:160579200-160581000	Weak transcription	H9 Derived Neuron 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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