Variant report

Variant	rs2886905
Chromosome Location	chr3:160492850-160492851
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	chr3:160475052..160477817-chr3:160492377..160494723,2	MCF-7	breast:
2	chr3:160484548..160486962-chr3:160492143..160493785,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12486979	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];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];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13073659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1378655	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1378656	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1378660	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1403048	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1455869	0.82[EUR][1000 genomes]
rs1598495	0.83[EUR][1000 genomes]
rs1829716	0.82[EUR][1000 genomes]
rs1851378	0.81[EUR][1000 genomes]
rs2049214	0.81[EUR][1000 genomes]
rs2049215	0.81[EUR][1000 genomes]
rs2367242	0.89[ASW][hapmap]
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];0.84[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6441331	0.84[AFR][1000 genomes];0.92[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];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791128	0.91[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs6794047	0.81[EUR][1000 genomes]
rs6805905	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7618832	0.83[EUR][1000 genomes]
rs7633816	0.95[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7634342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640231	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7640348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7642371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7643513	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7649322	0.87[AMR][1000 genomes]
rs7652749	0.87[AMR][1000 genomes]
rs897494	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs959960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[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]
rs972909	0.81[EUR][1000 genomes]
rs9809208	0.89[ASW][hapmap];1.00[YRI][hapmap]
rs9810290	0.89[ASW][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs9814394	0.83[EUR][1000 genomes]
rs9815499	0.83[EUR][1000 genomes]
rs9820796	0.91[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs9835634	0.91[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs9874183	0.87[AMR][1000 genomes]
rs9883862	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]
rs994966	0.87[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
rs2886905	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160475800-160497200	Weak transcription	Left Ventricle	heart
2	chr3:160476000-160496400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:160477600-160497000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:160477600-160498200	Weak transcription	Stomach Mucosa	stomach
5	chr3:160477800-160497800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:160484400-160496600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:160487200-160502200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:160490200-160495200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:160490200-160498200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:160490400-160496400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:160490400-160496400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:160490400-160496400	Weak transcription	Fetal Heart	heart
13	chr3:160490800-160494600	Enhancers	Stomach Smooth Muscle	stomach
14	chr3:160491200-160493200	Enhancers	Psoas Muscle	Psoas
15	chr3:160491400-160495600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:160492400-160493600	Enhancers	Colon Smooth Muscle	Colon
17	chr3:160492400-160498800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:160492600-160493200	Enhancers	Skeletal Muscle Female	skeletal muscle

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