Variant report

Variant	rs2044453
Chromosome Location	chr15:77423513-77423514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10519158	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11853633	0.89[ASN][1000 genomes]
rs11854182	0.89[ASN][1000 genomes]
rs11856513	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs11856538	0.96[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11857330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12148274	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12324366	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs12900110	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902106	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12902434	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12902446	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912963	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13379686	0.93[ASN][1000 genomes]
rs13380152	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1374201	0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs1446313	0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs16968730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17381652	0.96[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17381821	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17383078	0.85[ASN][1000 genomes]
rs17466480	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1867780	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2292594	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs34572155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35093280	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4592615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4638539	0.87[ASN][1000 genomes]
rs4886514	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886852	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs59831220	0.89[ASN][1000 genomes]
rs7163620	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7173670	0.89[ASN][1000 genomes]
rs7182221	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs74025074	0.93[ASN][1000 genomes]
rs7496431	0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2044453	PSTPIP1	cis	multi-tissue	Pritchard
rs2044453	PSTPIP1	cis	brain	seeQTL
rs2044453	CYP1A2	cis	cerebellum	SCAN
rs2044453	HMG20A	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77400200-77424200	Weak transcription	Esophagus	oesophagus
2	chr15:77400200-77427200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:77400200-77429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:77400400-77428600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:77400600-77425400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:77401600-77449600	Weak transcription	Colonic Mucosa	Colon
7	chr15:77404200-77430800	Weak transcription	Thymus	Thymus
8	chr15:77404600-77435600	Weak transcription	HMEC	breast
9	chr15:77407400-77424000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:77407400-77424400	Weak transcription	Aorta	Aorta
11	chr15:77407400-77425200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:77407400-77425200	Weak transcription	Liver	Liver
13	chr15:77407400-77425200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:77407400-77425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:77407400-77425400	Weak transcription	Gastric	stomach
16	chr15:77407600-77424000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:77407600-77424000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:77407600-77424200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:77407600-77424200	Weak transcription	Lung	lung
20	chr15:77407600-77425000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr15:77407600-77425200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr15:77407800-77425000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:77407800-77425400	Weak transcription	Pancreas	Pancrea
24	chr15:77408200-77424000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:77411400-77427000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:77411400-77427400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:77411800-77424200	Weak transcription	Fetal Muscle Leg	muscle
28	chr15:77411800-77424400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:77411800-77425200	Weak transcription	Dnd41	blood
30	chr15:77411800-77449400	Weak transcription	Colon Smooth Muscle	Colon
31	chr15:77412000-77424000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:77412000-77425000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:77412000-77425200	Weak transcription	Brain Angular Gyrus	brain
34	chr15:77412200-77425400	Weak transcription	Ovary	ovary
35	chr15:77412200-77425800	Weak transcription	Fetal Kidney	kidney
36	chr15:77412600-77435400	Weak transcription	HSMM	muscle
37	chr15:77412600-77435400	Weak transcription	NH-A	brain
38	chr15:77412800-77424800	Weak transcription	HUVEC	blood vessel
39	chr15:77412800-77425000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:77413000-77425200	Weak transcription	NHDF-Ad	bronchial
41	chr15:77413200-77425200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:77414400-77429600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:77416800-77427200	Weak transcription	GM12878-XiMat	blood
44	chr15:77417000-77427800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:77418600-77428000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:77418800-77431800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:77419400-77429200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:77419600-77424600	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:77419600-77425200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:77419600-77425400	Weak transcription	Brain Cingulate Gyrus	brain

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