Variant report

Variant	rs9883862
Chromosome Location	chr3:160527265-160527266
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160521593..160523754-chr3:160526329..160528531,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12486979	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12637922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13073659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1378654	0.83[EUR][1000 genomes]
rs1378655	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378656	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378657	0.83[EUR][1000 genomes]
rs1378660	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403048	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1851378	0.80[EUR][1000 genomes]
rs2049214	0.81[EUR][1000 genomes]
rs2049215	0.81[EUR][1000 genomes]
rs2367242	0.89[ASW][hapmap]
rs2886905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2886909	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441331	0.82[AMR][1000 genomes]
rs6781371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6791128	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs6794047	0.81[EUR][1000 genomes]
rs6805905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7633816	0.95[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs7634342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7640231	0.81[EUR][1000 genomes]
rs7640348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7643513	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs897494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959960	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]
rs972909	0.81[EUR][1000 genomes]
rs9809208	0.89[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9810290	0.89[ASW][hapmap];0.87[GIH][hapmap];0.83[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs9820796	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs9833075	0.83[EUR][1000 genomes]
rs9835634	0.91[CHB][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9883862	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160520400-160529600	Weak transcription	Colonic Mucosa	Colon
2	chr3:160522800-160527600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:160522800-160529000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:160523000-160532800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:160523200-160528600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:160523400-160527400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:160525200-160527400	Enhancers	Brain Germinal Matrix	brain
8	chr3:160525800-160528800	Enhancers	Liver	Liver
9	chr3:160525800-160529000	Enhancers	Brain Cingulate Gyrus	brain
10	chr3:160525800-160529000	Enhancers	Brain Hippocampus Middle	brain
11	chr3:160525800-160530200	Enhancers	Adipose Nuclei	Adipose
12	chr3:160525800-160530400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:160525800-160530600	Enhancers	Fetal Brain Female	brain
14	chr3:160525800-160530800	Enhancers	Fetal Brain Male	brain
15	chr3:160526000-160527800	Enhancers	Pancreas	Pancrea
16	chr3:160526000-160528000	Enhancers	Psoas Muscle	Psoas
17	chr3:160526000-160528200	Enhancers	Right Atrium	heart
18	chr3:160526000-160528400	Enhancers	Aorta	Aorta
19	chr3:160526000-160528400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr3:160526000-160528400	Enhancers	Left Ventricle	heart
21	chr3:160526000-160528600	Enhancers	Brain Substantia Nigra	brain
22	chr3:160526000-160528800	Enhancers	Brain Angular Gyrus	brain
23	chr3:160526000-160528800	Enhancers	Fetal Muscle Leg	muscle
24	chr3:160526000-160529200	Enhancers	Rectal Smooth Muscle	rectum
25	chr3:160526000-160530200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr3:160526000-160530600	Enhancers	Colon Smooth Muscle	Colon
27	chr3:160526200-160527400	Enhancers	Fetal Muscle Trunk	muscle
28	chr3:160526200-160528200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:160526200-160528600	Enhancers	Ovary	ovary
30	chr3:160526400-160527400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr3:160526400-160527600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:160526400-160528000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:160526400-160530600	Enhancers	Brain Anterior Caudate	brain
34	chr3:160526600-160528400	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr3:160526600-160529000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:160526600-160529800	Enhancers	NHDF-Ad	bronchial
37	chr3:160526600-160530400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:160526600-160530400	Weak transcription	Fetal Heart	heart
39	chr3:160526800-160529800	Weak transcription	Gastric	stomach
40	chr3:160527000-160527800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:160527000-160528000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:160527200-160527600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr3:160527200-160528600	Enhancers	Right Ventricle	heart
44	chr3:160527200-160528600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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