Variant report

Variant	rs17432566
Chromosome Location	chr2:63145409-63145410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12612046	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613453	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12614162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17347994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17432559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17473084	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17598689	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598881	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657533	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657580	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877027	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17432566	PEX13	cis	cerebellum	SCAN
rs17432566	OTX1	cis	Whole Blood	GTEx
rs17432566	TMEM17	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63102400-63146200	Weak transcription	Aorta	Aorta
2	chr2:63102600-63149800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:63102800-63150200	Weak transcription	Esophagus	oesophagus
4	chr2:63104000-63147800	Weak transcription	Fetal Stomach	stomach
5	chr2:63106000-63149600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:63106200-63149400	Weak transcription	Ovary	ovary
7	chr2:63107000-63150200	Weak transcription	HSMM	muscle
8	chr2:63107200-63146000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:63107200-63146000	Weak transcription	Left Ventricle	heart
10	chr2:63108200-63149200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:63108200-63149600	Weak transcription	Fetal Lung	lung
12	chr2:63122800-63166600	Weak transcription	HMEC	breast
13	chr2:63123000-63149400	Weak transcription	NHLF	lung
14	chr2:63123600-63146200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:63123600-63148800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:63123800-63149800	Weak transcription	NHEK	skin
17	chr2:63126200-63146000	Weak transcription	Primary T cells from cord blood	blood
18	chr2:63129400-63148800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:63131200-63148600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:63131400-63149800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:63131600-63149400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:63131800-63147000	Weak transcription	Liver	Liver
23	chr2:63133600-63149200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:63134800-63147200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:63135000-63147000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:63135400-63148600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:63137400-63147000	Weak transcription	HepG2	liver
28	chr2:63139200-63149800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:63140400-63148400	Weak transcription	Adipose Nuclei	Adipose
30	chr2:63140600-63149600	Weak transcription	NHDF-Ad	bronchial
31	chr2:63141000-63147200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:63142400-63190800	Weak transcription	Brain Angular Gyrus	brain
33	chr2:63144600-63145600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:63144600-63145600	Weak transcription	K562	blood
35	chr2:63144800-63147000	Weak transcription	A549	lung
36	chr2:63144800-63149600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:63144800-63149800	Weak transcription	Fetal Heart	heart
38	chr2:63145000-63145600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:63145000-63147200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:63145000-63149800	Weak transcription	Osteobl	bone
41	chr2:63145000-63155400	Weak transcription	HUVEC	blood vessel
42	chr2:63145200-63150200	Weak transcription	Lung	lung

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