Variant report

Variant	rs4552430
Chromosome Location	chr4:87434722-87434723
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10008165	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs10023787	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10029671	0.89[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs10031843	0.89[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1021101	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1026861	0.82[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap]
rs11097115	0.89[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11943428	0.82[ASN][1000 genomes]
rs11947018	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs11947775	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1481833	0.89[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs17011924	0.90[ASN][1000 genomes]
rs17418221	0.85[ASN][1000 genomes]
rs17418531	0.91[ASN][1000 genomes]
rs17418801	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17418878	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17419295	0.89[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs17419627	0.90[JPT][hapmap]
rs17419929	0.85[JPT][hapmap]
rs17452467	0.91[ASN][1000 genomes]
rs17452556	0.93[ASN][1000 genomes]
rs17453839	0.89[CHB][hapmap]
rs28483710	0.85[ASN][1000 genomes]
rs28485273	0.81[ASN][1000 genomes]
rs28529445	0.82[ASN][1000 genomes]
rs28534599	0.81[ASN][1000 genomes]
rs28663376	0.81[ASN][1000 genomes]
rs28735881	0.81[ASN][1000 genomes]
rs4235081	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4277747	0.88[ASN][1000 genomes]
rs4404513	0.92[ASN][1000 genomes]
rs4405982	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4407468	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4452393	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4466012	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4511966	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4513526	0.85[ASN][1000 genomes]
rs4529013	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607180	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4622964	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4640633	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693147	0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4693772	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4693776	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4693777	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55653332	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55654230	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55660529	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs55722156	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55746316	0.85[ASN][1000 genomes]
rs55757426	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55773619	0.85[ASN][1000 genomes]
rs55814693	0.82[ASN][1000 genomes]
rs55842318	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55872468	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55879246	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55881335	0.90[ASN][1000 genomes]
rs55908925	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55930543	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55969415	0.91[ASN][1000 genomes]
rs55982489	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56009992	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56150118	0.82[ASN][1000 genomes]
rs56164000	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56178389	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56222033	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56296936	0.85[ASN][1000 genomes]
rs56348925	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56353461	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59644743	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61152200	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6531932	0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs66669421	0.81[ASN][1000 genomes]
rs67274037	0.81[ASN][1000 genomes]
rs67341369	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67523832	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67928053	0.85[ASN][1000 genomes]
rs6822396	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6838659	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847139	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664002	0.91[ASN][1000 genomes]
rs72665711	0.96[ASN][1000 genomes]
rs72665712	0.96[ASN][1000 genomes]
rs72665714	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665719	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665722	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72665724	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72665725	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72665729	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665734	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665736	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665737	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665738	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665740	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665744	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665746	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665752	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665753	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72665756	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72665759	0.87[ASN][1000 genomes]
rs72665762	0.87[ASN][1000 genomes]
rs72665769	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72665771	0.85[ASN][1000 genomes]
rs72665772	0.82[ASN][1000 genomes]
rs72665777	0.81[ASN][1000 genomes]
rs7435744	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7673698	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7675845	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7679269	0.82[ASN][1000 genomes]
rs7694723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7695011	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7697819	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9307020	0.89[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9683663	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9993042	0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4552430	PTPN13	cis	parietal	SCAN
rs4552430	HPSE	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87430800-87434800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:87432000-87464800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:87434600-87435400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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