Variant report

Variant	rs1839017
Chromosome Location	chr3:160577670-160577671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12487861	0.85[JPT][hapmap]
rs12494732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080397	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1839019	0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1851378	0.85[JPT][hapmap]
rs1902282	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs4256178	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs6775743	0.84[JPT][hapmap]
rs6799058	0.85[YRI][hapmap]
rs718757	0.85[JPT][hapmap]
rs9809208	0.87[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap]
rs9810290	0.87[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9824439	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9831287	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]
rs9833075	0.84[JPT][hapmap]
rs9866566	0.85[JPT][hapmap]
rs9869116	0.88[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1839017	PPM1L	cis	cerebellum	SCAN
rs1839017	ARL14	cis	cerebellum	SCAN

Chromatin state (count:6 , 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	chr3:160575600-160578000	Weak transcription	Fetal Brain Female	brain
3	chr3:160576800-160578400	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr3:160576800-160578400	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr3:160577000-160579600	Weak transcription	Psoas Muscle	Psoas
6	chr3:160577200-160577800	Enhancers	Colon Smooth Muscle	Colon

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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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