Variant report

Variant	rs3775239
Chromosome Location	chr4:87631353-87631354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10003989	1.00[YRI][hapmap]
rs10008165	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs10016074	0.93[ASN][1000 genomes]
rs10019950	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10023787	0.88[GIH][hapmap];0.85[JPT][hapmap]
rs10029671	0.84[GIH][hapmap]
rs10033679	0.82[ASW][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1021101	0.81[GIH][hapmap]
rs1026861	0.88[GIH][hapmap]
rs1035191	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10516778	0.83[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs11097118	0.82[ASW][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap]
rs11097120	0.82[ASW][hapmap];0.88[MKK][hapmap];0.90[YRI][hapmap]
rs11930396	0.94[ASW][hapmap];0.82[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs11947018	0.84[CHD][hapmap];0.84[GIH][hapmap];0.80[ASN][1000 genomes]
rs12171458	0.81[ASN][1000 genomes]
rs12331502	0.97[ASN][1000 genomes]
rs12503659	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12510802	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13113689	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1420621	0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs1481833	0.84[GIH][hapmap]
rs17011986	0.81[ASN][1000 genomes]
rs17012072	0.84[JPT][hapmap]
rs17419627	0.81[GIH][hapmap]
rs17419929	0.81[GIH][hapmap]
rs17420607	0.83[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs17420966	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17454154	0.93[ASN][1000 genomes]
rs17454662	0.93[ASN][1000 genomes]
rs17694112	0.85[JPT][hapmap]
rs2006842	0.94[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2054592	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2054593	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2230600	0.85[JPT][hapmap];0.85[MEX][hapmap]
rs2287147	0.85[JPT][hapmap]
rs3775236	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775238	0.97[ASN][1000 genomes]
rs4263359	0.94[ASN][1000 genomes]
rs4693152	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4693780	0.94[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs57954319	0.86[ASN][1000 genomes]
rs6531932	0.88[GIH][hapmap];0.81[JPT][hapmap]
rs67867077	0.95[ASN][1000 genomes]
rs71605615	0.81[AFR][1000 genomes]
rs72665791	0.93[ASN][1000 genomes]
rs7664147	1.00[YRI][hapmap]
rs7664860	0.82[ASW][hapmap];0.92[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7688019	0.82[CEU][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs7698481	1.00[YRI][hapmap]
rs7699564	0.82[ASW][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs9307020	0.84[GIH][hapmap]
rs9307026	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs969734	0.84[CHB][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs9993042	0.80[GIH][hapmap]
rs9997453	1.00[YRI][hapmap];0.82[AFR][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3775239	PTPN13	cis	parietal	SCAN
rs3775239	PTPN13	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87574600-87644400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:87579200-87642600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:87579400-87644400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:87586400-87643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:87591800-87639000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:87591800-87641000	Weak transcription	Brain Anterior Caudate	brain
7	chr4:87592400-87656400	Weak transcription	Adipose Nuclei	Adipose
8	chr4:87593800-87641400	Weak transcription	Brain Angular Gyrus	brain
9	chr4:87594400-87642600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:87594400-87659800	Weak transcription	Ovary	ovary
11	chr4:87594800-87639200	Weak transcription	Fetal Kidney	kidney
12	chr4:87595200-87638200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:87595200-87651200	Weak transcription	Fetal Stomach	stomach
14	chr4:87600400-87639200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:87604800-87638200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:87606800-87641000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:87610400-87639600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:87611400-87638200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:87623400-87635400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:87623400-87641200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:87623400-87641200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:87623400-87643000	Weak transcription	Fetal Lung	lung
23	chr4:87623600-87636400	Weak transcription	NHDF-Ad	bronchial
24	chr4:87623600-87637000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:87623600-87639400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:87624800-87638600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:87625200-87635600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:87625200-87651600	Weak transcription	Esophagus	oesophagus
29	chr4:87625400-87638200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:87625400-87643400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:87628200-87631600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:87628400-87637200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:87628600-87634600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:87628600-87636600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:87628600-87638000	Weak transcription	HMEC	breast
36	chr4:87628800-87641600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:87628800-87641800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:87630400-87631600	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:87630400-87636400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:87630600-87631600	Enhancers	NHEK	skin
41	chr4:87631000-87637200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:87631200-87632200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:87631200-87712200	Weak transcription	Aorta	Aorta

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