Variant report

Variant	rs4646607
Chromosome Location	chr15:58285388-58285389
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58283520..58285614-chr15:58290103..58292837,2	K562	blood:

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10518961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1061278	0.82[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap]
rs1063666	0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs10851632	0.81[CEU][hapmap];0.94[CHB][hapmap]
rs11071363	0.93[ASN][1000 genomes]
rs11071364	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11071367	0.80[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11629553	0.82[ASN][1000 genomes]
rs11629583	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11631127	0.92[ASN][1000 genomes]
rs11636979	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11857465	0.94[ASN][1000 genomes]
rs12148281	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12324197	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12594082	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[ASN][1000 genomes]
rs12595180	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12595410	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12898976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12903724	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12905608	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12907125	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909865	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909979	0.84[ASN][1000 genomes]
rs12911450	0.94[ASN][1000 genomes]
rs12912093	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12914388	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12914414	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12914455	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12914603	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915508	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915821	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915989	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12917536	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1372369	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1441815	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1441819	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs1441829	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17820966	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17820990	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1812889	0.83[ASN][1000 genomes]
rs1822205	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1837851	0.91[ASN][1000 genomes]
rs1899355	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1994926	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1994927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2044071	0.92[ASN][1000 genomes]
rs2067062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2197092	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap]
rs2414527	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[ASN][1000 genomes]
rs2414529	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2414530	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[ASN][1000 genomes]
rs2642630	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2642632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2642636	0.81[CEU][hapmap]
rs2704196	0.94[ASN][1000 genomes]
rs2704197	0.92[ASN][1000 genomes]
rs2704218	0.85[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs2704225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2899611	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2899612	0.92[ASN][1000 genomes]
rs2899613	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3204690	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs33960206	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34226780	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34556514	0.93[ASN][1000 genomes]
rs34676542	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34958088	0.91[ASN][1000 genomes]
rs3742959	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs3742960	0.95[CHB][hapmap]
rs3742961	0.94[CHB][hapmap]
rs3784256	0.91[ASN][1000 genomes]
rs3784257	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[ASN][1000 genomes]
rs3784259	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[ASN][1000 genomes]
rs3784264	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3809535	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4144005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4238327	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4553566	0.92[ASN][1000 genomes]
rs4646549	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4646554	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4646555	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4646557	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4646559	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4646560	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4646564	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4646566	0.90[ASN][1000 genomes]
rs4646570	0.92[ASN][1000 genomes]
rs4646579	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4646580	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4646581	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646582	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646584	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646590	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646592	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646594	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646595	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646596	0.96[ASN][1000 genomes]
rs4646597	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646598	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646600	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646602	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646603	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4646623	0.85[ASN][1000 genomes]
rs4646625	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[ASN][1000 genomes]
rs4646626	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[ASN][1000 genomes]
rs4646642	0.81[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap]
rs57975858	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493977	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6493978	0.94[ASN][1000 genomes]
rs6493979	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6493980	0.91[ASN][1000 genomes]
rs6493981	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs66971399	0.94[ASN][1000 genomes]
rs7171261	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[ASN][1000 genomes]
rs7171714	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7178598	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7180059	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8023769	0.92[ASN][1000 genomes]
rs8026952	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8027188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8027964	0.92[ASN][1000 genomes]
rs8032572	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8041644	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9635346	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9635350	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv833023	chr15:58161839-58340174	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv569593	chr15:58201698-58308650	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv904261	chr15:58258424-58347260	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4646607	PYGO1	cis	cerebellum	SCAN
rs4646607	MNS1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58262600-58287800	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:58283600-58289000	Strong transcription	K562	blood
3	chr15:58284000-58285400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr15:58284400-58288600	Enhancers	Fetal Lung	lung
5	chr15:58284600-58285400	Enhancers	HUVEC	blood vessel
6	chr15:58284600-58287000	Genic enhancers	Fetal Kidney	kidney
7	chr15:58284800-58287400	Enhancers	Fetal Stomach	stomach
8	chr15:58284800-58287400	Enhancers	Ovary	ovary
9	chr15:58285200-58285800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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