Variant report

Variant	rs9307020
Chromosome Location	chr4:87543847-87543848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10008165	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]
rs10023787	0.90[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029671	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10030525	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10031843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1021101	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1026861	0.90[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1035191	0.84[GIH][hapmap]
rs10516778	0.84[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap]
rs11097115	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11943428	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11947018	0.90[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1420621	0.85[CEU][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs1481833	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011986	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17419295	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17419627	0.88[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17419929	0.88[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17420607	0.86[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap]
rs17453839	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2006842	0.84[GIH][hapmap]
rs2054592	0.80[JPT][hapmap]
rs2054593	0.81[GIH][hapmap]
rs28483710	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28485273	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28529445	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28534599	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535527	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28663376	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28678816	0.98[ASN][1000 genomes]
rs28735881	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775239	0.84[GIH][hapmap]
rs4235081	0.81[ASN][1000 genomes]
rs4277747	0.90[ASN][1000 genomes]
rs4405982	0.82[ASN][1000 genomes]
rs4407468	0.82[ASN][1000 genomes]
rs4452393	0.84[ASN][1000 genomes]
rs4466012	0.82[ASN][1000 genomes]
rs4511966	0.84[ASN][1000 genomes]
rs4513526	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4529013	0.89[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4552430	0.81[ASN][1000 genomes]
rs4607180	0.82[ASN][1000 genomes]
rs4622964	0.82[ASN][1000 genomes]
rs4693147	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs4693776	0.82[ASN][1000 genomes]
rs4693777	0.81[ASN][1000 genomes]
rs4693780	0.91[GIH][hapmap];0.80[JPT][hapmap]
rs55640323	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs55654230	0.92[ASN][1000 genomes]
rs55746316	0.95[ASN][1000 genomes]
rs55757426	0.95[ASN][1000 genomes]
rs55773619	0.95[ASN][1000 genomes]
rs55842318	0.82[ASN][1000 genomes]
rs55872468	0.82[ASN][1000 genomes]
rs55879246	0.95[ASN][1000 genomes]
rs55908925	0.82[ASN][1000 genomes]
rs55930543	0.82[ASN][1000 genomes]
rs55978957	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs55982489	0.82[ASN][1000 genomes]
rs56009992	0.82[ASN][1000 genomes]
rs56150118	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs56164000	0.81[ASN][1000 genomes]
rs56178389	0.94[ASN][1000 genomes]
rs56296936	0.95[ASN][1000 genomes]
rs56348925	0.94[ASN][1000 genomes]
rs56353461	0.81[ASN][1000 genomes]
rs59644743	0.81[ASN][1000 genomes]
rs61152200	0.82[ASN][1000 genomes]
rs6531932	0.90[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66669421	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67274037	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67341369	0.90[ASN][1000 genomes]
rs67523832	0.92[ASN][1000 genomes]
rs67928053	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6822396	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs6838659	0.89[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs6847139	0.89[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs72665722	0.81[ASN][1000 genomes]
rs72665724	0.80[ASN][1000 genomes]
rs72665725	0.81[ASN][1000 genomes]
rs72665729	0.82[ASN][1000 genomes]
rs72665734	0.82[ASN][1000 genomes]
rs72665736	0.82[ASN][1000 genomes]
rs72665737	0.82[ASN][1000 genomes]
rs72665738	0.82[ASN][1000 genomes]
rs72665740	0.81[ASN][1000 genomes]
rs72665744	0.82[ASN][1000 genomes]
rs72665746	0.81[ASN][1000 genomes]
rs72665752	0.82[ASN][1000 genomes]
rs72665753	0.84[ASN][1000 genomes]
rs72665756	0.84[ASN][1000 genomes]
rs72665759	0.94[ASN][1000 genomes]
rs72665762	0.94[ASN][1000 genomes]
rs72665769	0.92[ASN][1000 genomes]
rs72665771	0.95[ASN][1000 genomes]
rs72665772	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72665777	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7435744	0.84[ASN][1000 genomes]
rs7694723	0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs969734	0.84[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs9993042	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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
rs9307020	PTPN13	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87521400-87546800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:87531000-87553600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:87536600-87547000	Weak transcription	Fetal Kidney	kidney
4	chr4:87538000-87546200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:87540400-87554000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:87540400-87556200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr4:87541000-87545600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:87541200-87545600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:87541200-87548800	Weak transcription	NHEK	skin
10	chr4:87541200-87553400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:87541200-87571200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:87541600-87548800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:87541600-87556200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:87541800-87544000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:87542200-87544200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr4:87542400-87544400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:87542400-87548600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:87542800-87545600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:87542800-87557600	Weak transcription	Brain Anterior Caudate	brain
20	chr4:87542800-87566400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:87543000-87547000	Weak transcription	Fetal Lung	lung
22	chr4:87543000-87553200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:87543200-87545600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:87543200-87556400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:87543600-87544400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:87543800-87544200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr4:87543800-87544200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:87543800-87545600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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