Variant report

Variant	rs10008165
Chromosome Location	chr4:87570458-87570459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10023787	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10029671	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10030525	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10031843	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1021101	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1026861	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1035191	0.87[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10516778	0.91[GIH][hapmap]
rs11097115	0.94[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs11943428	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11947018	0.90[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12503659	0.81[ASN][1000 genomes]
rs12510802	0.81[ASN][1000 genomes]
rs13113689	0.81[ASN][1000 genomes]
rs1420621	0.85[CEU][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs1481833	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17011986	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17419295	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17419627	0.84[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17419929	0.84[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17420607	0.91[GIH][hapmap]
rs17453839	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2006842	0.84[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2054593	0.81[GIH][hapmap];0.81[JPT][hapmap]
rs28483710	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28485273	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28529445	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28534599	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28535527	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28663376	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28678816	0.89[ASN][1000 genomes]
rs28735881	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775236	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs3775239	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs4277747	0.83[ASN][1000 genomes]
rs4513526	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4529013	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs4693147	0.89[CHB][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap]
rs4693780	0.91[GIH][hapmap]
rs55640323	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55654230	0.89[ASN][1000 genomes]
rs55746316	0.86[ASN][1000 genomes]
rs55757426	0.86[ASN][1000 genomes]
rs55773619	0.86[ASN][1000 genomes]
rs55879246	0.86[ASN][1000 genomes]
rs55978957	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56150118	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56178389	0.90[ASN][1000 genomes]
rs56296936	0.86[ASN][1000 genomes]
rs56348925	0.84[ASN][1000 genomes]
rs6531932	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66669421	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67274037	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67341369	0.87[ASN][1000 genomes]
rs67523832	0.89[ASN][1000 genomes]
rs67928053	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6822396	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs6838659	0.82[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap]
rs6847139	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs72665759	0.84[ASN][1000 genomes]
rs72665762	0.84[ASN][1000 genomes]
rs72665769	0.89[ASN][1000 genomes]
rs72665771	0.86[ASN][1000 genomes]
rs72665772	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72665777	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7694723	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9307020	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs969734	0.87[GIH][hapmap]
rs9993042	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv879523	chr4:87517609-87594472	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv879524	chr4:87517609-87603929	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv2755470	chr4:87536515-87613212	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10008165	PTPN13	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87541200-87571200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:87544400-87571200	Weak transcription	Pancreas	Pancrea
3	chr4:87556200-87570800	Weak transcription	Fetal Stomach	stomach
4	chr4:87557600-87571000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:87557600-87571200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:87563000-87571000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:87564400-87570800	Weak transcription	Fetal Intestine Small	intestine
8	chr4:87566400-87571200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:87566400-87578400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:87566600-87570800	Weak transcription	NHEK	skin
11	chr4:87566600-87571200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:87566600-87578600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:87567000-87571400	Weak transcription	NHDF-Ad	bronchial
14	chr4:87567800-87571200	Weak transcription	Esophagus	oesophagus
15	chr4:87568600-87571400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:87568800-87571800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:87568800-87573400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:87568800-87575200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:87569400-87571400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:87569400-87571800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:87569800-87571800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:87570000-87571000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:87570000-87571200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:87570200-87570600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:87570200-87571400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:87570400-87571600	ZNF genes & repeats	Fetal Lung	lung

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