Variant report

Variant	rs959960
Chromosome Location	chr3:160469056-160469057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160468850..160470380-chr3:160471607..160473600,2	K562	blood:
2	chr3:160467646..160471056-chr3:160471493..160474587,3	K562	blood:

Variant related genes	Relation type
ENSG00000163590	Chromatin interaction
ENSG00000260572	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12486979	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12637922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs13073659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1378655	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1378656	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1378660	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1403048	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1455869	0.80[EUR][1000 genomes]
rs1829716	0.80[EUR][1000 genomes]
rs2886905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2886909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6441331	0.96[AMR][1000 genomes]
rs6781371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6791128	0.91[CHB][hapmap];0.86[AMR][1000 genomes]
rs6805905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7633816	0.95[CHB][hapmap];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7634342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7640231	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7640348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7642371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7643513	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7649322	0.90[AMR][1000 genomes]
rs7652749	0.90[AMR][1000 genomes]
rs897494	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9810290	0.80[GIH][hapmap];0.83[TSI][hapmap]
rs9820796	0.91[CHB][hapmap];0.90[AMR][1000 genomes]
rs9835634	0.91[CHB][hapmap];0.90[AMR][1000 genomes]
rs9874183	0.90[AMR][1000 genomes]
rs9883862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs994966	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs959960	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160465400-160471400	Weak transcription	Fetal Brain Male	brain
2	chr3:160465800-160472200	Weak transcription	Hela-S3	cervix
3	chr3:160466000-160470600	Weak transcription	Brain Anterior Caudate	brain
4	chr3:160466000-160471200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:160466000-160472000	Weak transcription	Gastric	stomach
6	chr3:160466000-160472000	Weak transcription	Psoas Muscle	Psoas
7	chr3:160466200-160471200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:160466200-160471400	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:160466200-160472000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:160466200-160472000	Weak transcription	Left Ventricle	heart
11	chr3:160466400-160470000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:160466400-160470800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:160466400-160471200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:160466400-160471200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:160466400-160471400	Weak transcription	Adipose Nuclei	Adipose
16	chr3:160466400-160471400	Weak transcription	Brain Substantia Nigra	brain
17	chr3:160466800-160471400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:160467200-160470000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:160467200-160471200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:160467400-160471600	Weak transcription	Liver	Liver
21	chr3:160467400-160472000	Weak transcription	Pancreas	Pancrea
22	chr3:160467600-160470600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:160468800-160471800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:160469000-160471400	Weak transcription	Fetal Stomach	stomach

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