Variant report

Variant	rs4277747
Chromosome Location	chr4:87500298-87500299
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10008165	0.94[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10023787	0.94[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10029671	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap]
rs10030525	0.84[ASN][1000 genomes]
rs10031843	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1021101	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1026861	0.94[CHB][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10516778	0.81[CHD][hapmap];0.83[GIH][hapmap]
rs11097115	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11943428	0.87[ASN][1000 genomes]
rs11947018	0.83[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs11947775	0.86[ASN][1000 genomes]
rs1420621	0.87[GIH][hapmap]
rs1481833	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17011924	0.80[ASN][1000 genomes]
rs17418221	0.85[CEU][hapmap];0.81[ASN][1000 genomes]
rs17418531	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17418801	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17418878	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17419295	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17419627	0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap]
rs17419929	1.00[ASW][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs17420607	0.84[CHD][hapmap];0.83[GIH][hapmap]
rs17452467	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17452556	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17453839	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs28483710	0.90[ASN][1000 genomes]
rs28485273	0.90[ASN][1000 genomes]
rs28529445	0.92[ASN][1000 genomes]
rs28534599	0.90[ASN][1000 genomes]
rs28535527	0.84[ASN][1000 genomes]
rs28663376	0.90[ASN][1000 genomes]
rs28678816	0.89[ASN][1000 genomes]
rs28735881	0.90[ASN][1000 genomes]
rs4235081	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4404513	0.82[ASN][1000 genomes]
rs4405982	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4407468	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4452393	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4466012	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4511966	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4513526	0.90[ASN][1000 genomes]
rs4529013	0.89[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4552430	0.88[ASN][1000 genomes]
rs4607180	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4622964	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4640633	0.86[ASN][1000 genomes]
rs4693147	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4693772	0.86[ASN][1000 genomes]
rs4693776	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4693777	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4693780	0.83[GIH][hapmap]
rs55640323	0.84[ASN][1000 genomes]
rs55653332	0.86[ASN][1000 genomes]
rs55654230	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55660529	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55722156	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55746316	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55757426	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55773619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55842318	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55872468	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55879246	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55881335	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55908925	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55930543	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55969415	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55978957	0.84[ASN][1000 genomes]
rs55982489	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56009992	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56150118	0.92[ASN][1000 genomes]
rs56164000	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56178389	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56222033	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56296936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56348925	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56353461	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59644743	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61152200	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6531932	0.94[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs66669421	0.90[ASN][1000 genomes]
rs67274037	0.90[ASN][1000 genomes]
rs67341369	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67523832	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67928053	0.90[ASN][1000 genomes]
rs6822396	0.89[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6838659	0.89[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs6847139	0.89[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72664002	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665711	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72665712	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72665714	0.86[ASN][1000 genomes]
rs72665719	0.86[ASN][1000 genomes]
rs72665722	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72665724	0.88[ASN][1000 genomes]
rs72665725	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72665729	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665734	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665736	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665737	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665738	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665740	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72665744	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665746	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72665752	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665753	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665756	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665759	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665762	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665769	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72665771	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72665772	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs72665777	0.90[ASN][1000 genomes]
rs7435744	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7673698	0.86[ASN][1000 genomes]
rs7694723	0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7695011	0.86[ASN][1000 genomes]
rs7697819	0.84[ASN][1000 genomes]
rs9307020	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9683663	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs969734	0.81[CHD][hapmap]
rs9993042	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4277747	HPSE	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87480600-87502000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:87480800-87501800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:87493800-87507000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr4:87496600-87512600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:87498800-87508600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:87499000-87502200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:87499600-87502800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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