Variant report

Variant	rs1420621
Chromosome Location	chr4:87632672-87632673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10000891	1.00[YRI][hapmap]
rs10001986	1.00[YRI][hapmap]
rs10008165	0.85[CEU][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs10016074	0.93[ASN][1000 genomes]
rs10019950	0.93[ASN][1000 genomes]
rs10020590	1.00[YRI][hapmap]
rs10023163	1.00[YRI][hapmap]
rs10023787	0.91[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs10029565	1.00[YRI][hapmap]
rs10029671	0.85[CEU][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.89[TSI][hapmap]
rs10031843	0.85[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs10033029	1.00[YRI][hapmap]
rs1021101	0.91[GIH][hapmap];0.80[JPT][hapmap]
rs1026861	0.91[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs1035191	1.00[ASW][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs10470933	1.00[YRI][hapmap]
rs10516778	0.89[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10516780	1.00[YRI][hapmap]
rs11097115	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs11930396	0.85[JPT][hapmap]
rs11947018	0.87[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs12331502	0.97[ASN][1000 genomes]
rs12498681	1.00[YRI][hapmap]
rs12499575	1.00[YRI][hapmap]
rs12503659	0.93[ASN][1000 genomes]
rs12508339	1.00[YRI][hapmap]
rs12510802	0.90[ASN][1000 genomes]
rs12512858	1.00[YRI][hapmap]
rs13111757	1.00[YRI][hapmap]
rs13113689	0.84[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs13136651	1.00[YRI][hapmap]
rs1420620	1.00[YRI][hapmap]
rs1481833	0.85[CEU][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs17011986	0.80[EUR][1000 genomes]
rs17012072	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs17419295	0.80[JPT][hapmap]
rs17419627	0.83[CHD][hapmap];0.91[GIH][hapmap];0.80[ASN][1000 genomes]
rs17419929	0.83[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs17420607	0.89[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17420966	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17453839	0.84[JPT][hapmap]
rs17454154	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17454432	1.00[YRI][hapmap]
rs17454655	1.00[YRI][hapmap]
rs17454662	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17694112	0.85[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs2006842	0.85[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[ASN][1000 genomes]
rs2054592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2054593	1.00[ASW][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs2230600	0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2287147	0.85[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs28534599	0.83[EUR][1000 genomes]
rs28663376	0.83[EUR][1000 genomes]
rs28735881	0.83[EUR][1000 genomes]
rs3775236	0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3775238	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3775239	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]
rs4263359	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4693152	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4693780	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs57954319	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6531932	0.91[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs67867077	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72665791	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7688019	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs9307020	0.85[CEU][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs9307026	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs969734	0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9993042	0.85[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1420621	PTPN13	cis	parietal	SCAN

Chromatin state (count:42 , 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	chr4:87628400-87637200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:87628600-87634600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:87628600-87636600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:87628600-87638000	Weak transcription	HMEC	breast
35	chr4:87628800-87641600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:87628800-87641800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:87630400-87636400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:87631000-87637200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
40	chr4:87631600-87634200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:87631600-87636800	Weak transcription	NHEK	skin
42	chr4:87632200-87633600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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