Variant report

Variant	rs955038
Chromosome Location	chr2:183453245-183453246
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:25)

rs_ID	r²[population]
rs10189650	0.80[ASN][1000 genomes]
rs10207865	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10211307	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10497610	0.80[ASN][1000 genomes]
rs12693315	0.93[ASN][1000 genomes]
rs12693316	0.93[ASN][1000 genomes]
rs12693317	0.93[ASN][1000 genomes]
rs12693318	0.80[ASN][1000 genomes]
rs12990399	0.93[ASN][1000 genomes]
rs13382205	0.80[ASN][1000 genomes]
rs13389338	0.93[ASN][1000 genomes]
rs13389590	0.80[ASN][1000 genomes]
rs13416838	0.80[ASN][1000 genomes]
rs13419447	0.80[ASN][1000 genomes]
rs13419727	0.80[ASN][1000 genomes]
rs13420165	0.80[ASN][1000 genomes]
rs13423751	0.80[ASN][1000 genomes]
rs13426633	0.80[ASN][1000 genomes]
rs13432896	0.80[ASN][1000 genomes]
rs2049666	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2368330	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35272130	0.80[ASN][1000 genomes]
rs35750735	0.93[ASN][1000 genomes]
rs6758080	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7570144	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533782	chr2:183059730-183500040	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2830429	chr2:183300759-183545378	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv875479	chr2:183442443-183482466	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv875480	chr2:183442443-183489249	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv1837855	chr2:183452578-183499313	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs955038	PDE1A	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183451000-183453400	Enhancers	NHDF-Ad	bronchial
2	chr2:183451200-183453400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:183451600-183453400	Enhancers	NHLF	lung
4	chr2:183451800-183453400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:183451800-183453400	Enhancers	NH-A	brain
6	chr2:183451800-183453400	Enhancers	Osteobl	bone
7	chr2:183452000-183456200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:183452000-183457600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:183452000-183457800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:183452200-183456400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:183452200-183456600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:183452200-183457800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:183452800-183456000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:183452800-183456800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:183453000-183453400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:183453000-183453400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:183453000-183456000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:183453000-183456000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:183453000-183457600	Weak transcription	HMEC	breast
20	chr2:183453000-183457600	Weak transcription	HSMM	muscle
21	chr2:183453000-183457800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:183453200-183456000	Weak transcription	HSMMtube	muscle
23	chr2:183453200-183457600	Weak transcription	NHEK	skin
24	chr2:183453200-183457800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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