Variant report

Variant	rs2306061
Chromosome Location	chr3:160787502-160787503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160786415..160790259-chr3:161088559..161091068,4	MCF-7	breast:
2	chr3:160786229..160788544-chr3:160938497..160940062,2	MCF-7	breast:
3	chr3:160786404..160789728-chr3:161132273..161134989,3	MCF-7	breast:
4	chr3:160784766..160787646-chr3:161137298..161141604,4	MCF-7	breast:
5	chr3:160786642..160788388-chr3:160816154..160818351,2	MCF-7	breast:
6	chr3:160785968..160788814-chr3:160790660..160793617,2	K562	blood:
7	chr3:160787358..160789426-chr3:161053808..161055852,2	MCF-7	breast:
8	chr3:160786158..160788283-chr3:160805883..160807587,2	K562	blood:
9	chr3:160783848..160785805-chr3:160786120..160789700,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1026572	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs1037888	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10513559	0.85[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs10513562	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11708813	0.85[CEU][hapmap]
rs11716265	0.85[CEU][hapmap]
rs11922752	0.85[CEU][hapmap]
rs12493960	0.82[AMR][1000 genomes]
rs12639128	0.85[CEU][hapmap]
rs13064176	0.85[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs13066683	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13086250	0.85[CEU][hapmap]
rs13089559	0.85[CEU][hapmap]
rs13092102	0.85[CEU][hapmap]
rs13098884	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1374793	0.84[CEU][hapmap]
rs1447618	0.85[CEU][hapmap]
rs1447619	0.85[CEU][hapmap]
rs1447620	0.85[CEU][hapmap]
rs1599374	0.93[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs1599376	0.82[AMR][1000 genomes]
rs1599378	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1599381	0.81[EUR][1000 genomes]
rs1599383	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1599386	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1599389	0.81[EUR][1000 genomes]
rs1599390	0.81[EUR][1000 genomes]
rs1609688	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1610158	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236725	0.85[CEU][hapmap]
rs17236746	0.85[CEU][hapmap]
rs17826438	0.89[CEU][hapmap]
rs2121718	0.85[CEU][hapmap]
rs2593812	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4342141	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes]
rs4370045	0.85[MEX][hapmap];0.84[TSI][hapmap]
rs4414866	0.84[CEU][hapmap]
rs4557202	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs4597724	0.84[TSI][hapmap]
rs4616689	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4618258	0.85[CEU][hapmap]
rs4679662	0.85[CEU][hapmap]
rs4679666	0.84[CEU][hapmap]
rs4679671	0.84[EUR][1000 genomes]
rs4679922	0.85[CEU][hapmap]
rs4679924	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs4679926	0.88[CEU][hapmap]
rs5004752	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62280333	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6441339	0.85[CEU][hapmap]
rs6441354	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs6764019	0.85[CEU][hapmap]
rs6765270	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6769642	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6772578	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6774635	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6775627	0.82[TSI][hapmap]
rs6783085	0.81[EUR][1000 genomes]
rs6786871	0.80[EUR][1000 genomes]
rs6789244	0.81[EUR][1000 genomes]
rs6789388	0.80[MEX][hapmap];0.80[TSI][hapmap]
rs6794601	0.84[TSI][hapmap]
rs6799130	0.80[EUR][1000 genomes]
rs6804650	0.85[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs6806054	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6809177	0.85[CEU][hapmap]
rs7614375	0.81[EUR][1000 genomes]
rs7617204	0.81[EUR][1000 genomes]
rs7619011	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7622047	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7628880	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7630674	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7630768	0.81[EUR][1000 genomes]
rs7632423	0.85[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7633857	0.81[EUR][1000 genomes]
rs7637086	0.81[EUR][1000 genomes]
rs7647285	0.81[EUR][1000 genomes]
rs7650703	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7651087	0.81[EUR][1000 genomes]
rs778642	0.85[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778643	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778645	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778646	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778649	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778653	0.85[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs778654	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778657	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs778663	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs796609	0.85[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs898680	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs898681	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9290065	0.92[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9290069	0.80[CEU][hapmap]
rs9790132	0.85[CEU][hapmap]
rs980975	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs980976	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9811594	0.85[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9820825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9831488	0.86[MEX][hapmap]
rs9847866	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9848239	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9860360	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9867582	0.85[EUR][1000 genomes]
rs9875200	0.85[CEU][hapmap];0.84[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2306061	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160777200-160787800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:160780400-160788600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:160780800-160821400	Weak transcription	Fetal Brain Male	brain
4	chr3:160781400-160803400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:160781600-160788000	Weak transcription	Psoas Muscle	Psoas
6	chr3:160781600-160791000	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:160781800-160798200	Weak transcription	Fetal Stomach	stomach
8	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
9	chr3:160782000-160799800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:160782800-160795000	Weak transcription	Right Ventricle	heart
11	chr3:160783400-160788600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:160784000-160789400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:160784200-160799000	Weak transcription	Ovary	ovary
14	chr3:160784400-160788800	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:160785000-160789000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:160785400-160788600	Enhancers	Pancreas	Pancrea
17	chr3:160785400-160788800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr3:160785600-160787800	Weak transcription	Adipose Nuclei	Adipose
19	chr3:160785800-160789000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:160786200-160788400	Enhancers	Placenta	Placenta
21	chr3:160786200-160788800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:160786400-160788000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:160786400-160788000	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:160786400-160788200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:160786600-160788600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:160786600-160789000	Enhancers	Dnd41	blood
27	chr3:160786600-160789600	Enhancers	HUVEC	blood vessel
28	chr3:160786600-160790000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr3:160786800-160788200	Flanking Active TSS	GM12878-XiMat	blood
30	chr3:160786800-160789200	Enhancers	Primary hematopoietic stem cells	blood
31	chr3:160787000-160788800	Enhancers	Stomach Mucosa	stomach
32	chr3:160787000-160789400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:160787000-160789400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
35	chr3:160787200-160787600	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr3:160787200-160787600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:160787200-160787600	Enhancers	Gastric	stomach
38	chr3:160787200-160787800	Enhancers	Fetal Intestine Small	intestine
39	chr3:160787200-160788200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:160787200-160788200	Enhancers	Brain Cingulate Gyrus	brain
41	chr3:160787200-160788200	Enhancers	Fetal Brain Female	brain
42	chr3:160787200-160788200	Enhancers	Lung	lung
43	chr3:160787200-160788200	Enhancers	HSMM	muscle
44	chr3:160787200-160788200	Enhancers	NHDF-Ad	bronchial
45	chr3:160787200-160788400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:160787200-160788400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:160787200-160788400	Enhancers	NH-A	brain
48	chr3:160787200-160788600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:160787200-160788600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:160787200-160788600	Enhancers	Brain Angular Gyrus	brain

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