Variant report

Variant	rs654466
Chromosome Location	chr18:43594816-43594817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10468860	0.81[JPT][hapmap]
rs10502871	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11082506	0.94[ASN][1000 genomes]
rs12606939	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12607686	0.80[ASN][1000 genomes]
rs16978509	0.82[JPT][hapmap]
rs16978516	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16978517	0.98[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs488431	0.82[JPT][hapmap]
rs4890310	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4890612	0.82[JPT][hapmap]
rs4890613	0.95[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4890614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890615	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs57141604	0.88[ASN][1000 genomes]
rs58563731	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs593664	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs609331	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs610186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61423911	0.93[ASN][1000 genomes]
rs6507659	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs6507660	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6507661	0.87[ASN][1000 genomes]
rs6507662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68061103	0.99[ASN][1000 genomes]
rs687526	0.93[CHD][hapmap];0.82[JPT][hapmap]
rs688547	0.93[CHD][hapmap];0.82[JPT][hapmap]
rs8097830	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9675392	0.93[CEU][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.89[EUR][1000 genomes];0.81[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	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs654466	PSTPIP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43558800-43608000	Weak transcription	Pancreas	Pancrea
2	chr18:43560400-43597600	Weak transcription	Left Ventricle	heart
3	chr18:43568600-43596800	Weak transcription	Adipose Nuclei	Adipose
4	chr18:43568800-43607800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr18:43571400-43622000	Weak transcription	Gastric	stomach
6	chr18:43574200-43597400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr18:43574200-43608000	Weak transcription	NHLF	lung
8	chr18:43574600-43608000	Weak transcription	Osteobl	bone
9	chr18:43583400-43607800	Weak transcription	Fetal Intestine Small	intestine
10	chr18:43583400-43608200	Weak transcription	Esophagus	oesophagus
11	chr18:43586200-43607600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr18:43587200-43599800	Weak transcription	Fetal Intestine Large	intestine
13	chr18:43588000-43607400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr18:43589200-43599000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr18:43589200-43607800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr18:43590800-43600600	Weak transcription	K562	blood
17	chr18:43590800-43601600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr18:43590800-43607800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr18:43590800-43608000	Weak transcription	Primary T cells from cord blood	blood
20	chr18:43591000-43595000	Weak transcription	Aorta	Aorta
21	chr18:43591000-43595000	Weak transcription	Spleen	Spleen
22	chr18:43591000-43600000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr18:43591000-43606200	Weak transcription	HMEC	breast
24	chr18:43591000-43607800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr18:43591000-43607800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr18:43591000-43608000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr18:43591000-43608000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr18:43591000-43608000	Weak transcription	Ovary	ovary
29	chr18:43591200-43595000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr18:43591200-43595200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr18:43591200-43607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr18:43591600-43602200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr18:43591600-43608000	Weak transcription	NHEK	skin
34	chr18:43592600-43597000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr18:43593000-43595000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr18:43593200-43595000	Enhancers	GM12878-XiMat	blood
37	chr18:43593800-43595800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr18:43594000-43595400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr18:43594000-43595800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr18:43594000-43597000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr18:43594200-43607400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr18:43594400-43595000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr18:43594400-43595800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr18:43594600-43599600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr18:43594800-43595000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr18:43594800-43595200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr18:43594800-43595600	Strong transcription	Liver	Liver
48	chr18:43594800-43595600	Strong transcription	Lung	lung
49	chr18:43594800-43598000	Strong transcription	Monocytes-CD14+_RO01746	blood

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