Variant report

Variant	rs6493979
Chromosome Location	chr15:58338052-58338053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58036135..58038062-chr15:58336586..58339373,2	K562	blood:
2	chr15:58336832..58338668-chr15:58341480..58343380,2	K562	blood:
3	chr15:58337253..58339004-chr15:58345727..58347852,2	K562	blood:
4	chr15:58337544..58340240-chr15:58358497..58360223,2	K562	blood:

Variant related genes	Relation type
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10518961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1061278	0.95[CHB][hapmap];0.86[GIH][hapmap]
rs1063666	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs10851632	0.94[CHB][hapmap]
rs11071363	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071364	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071367	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11629553	0.84[ASN][1000 genomes]
rs11629583	0.90[ASN][1000 genomes]
rs11631127	0.91[ASN][1000 genomes]
rs11636979	0.94[ASN][1000 genomes]
rs11857465	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12148281	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12324197	0.91[ASN][1000 genomes]
rs12594082	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12595180	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12595410	0.94[ASN][1000 genomes]
rs12898976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12903724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12905608	0.95[ASN][1000 genomes]
rs12907125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12909423	0.83[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs12909865	0.94[ASN][1000 genomes]
rs12909979	0.83[ASN][1000 genomes]
rs12911450	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12914388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12914414	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12914455	0.95[ASN][1000 genomes]
rs12914603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12915508	0.91[ASN][1000 genomes]
rs12915821	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12915989	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12917536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1372369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1441815	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1441819	0.95[CHB][hapmap]
rs1441829	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17820966	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17820990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1812889	0.81[ASN][1000 genomes]
rs1822205	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1837851	0.90[ASN][1000 genomes]
rs1899355	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1994926	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1994927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2044071	0.91[ASN][1000 genomes]
rs2067062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2197092	0.95[CHB][hapmap];0.88[GIH][hapmap]
rs2414527	0.95[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2414529	0.95[ASN][1000 genomes]
rs2414530	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2642630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2642632	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2704196	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2704197	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704218	0.85[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap];0.90[ASN][1000 genomes]
rs2704225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2899611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2899612	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2899613	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3204690	0.95[CHB][hapmap];0.86[GIH][hapmap]
rs33960206	0.95[ASN][1000 genomes]
rs34226780	0.98[ASN][1000 genomes]
rs34556514	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34676542	0.98[ASN][1000 genomes]
rs34958088	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742959	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap]
rs3742960	0.95[CHB][hapmap]
rs3742961	0.94[CHB][hapmap]
rs3784256	0.88[ASN][1000 genomes]
rs3784257	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3784259	0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3784264	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809535	0.89[ASN][1000 genomes]
rs4144005	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4238327	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4553566	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646549	0.90[ASN][1000 genomes]
rs4646554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[ASN][1000 genomes]
rs4646555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4646557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4646559	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4646560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4646564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs4646566	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4646570	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4646580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4646581	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4646582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4646584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4646588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4646589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4646590	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[ASN][1000 genomes]
rs4646592	0.93[ASN][1000 genomes]
rs4646594	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[ASN][1000 genomes]
rs4646595	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[ASN][1000 genomes]
rs4646596	0.95[ASN][1000 genomes]
rs4646597	0.95[ASN][1000 genomes]
rs4646598	0.97[ASN][1000 genomes]
rs4646600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4646602	0.94[ASN][1000 genomes]
rs4646603	0.96[ASN][1000 genomes]
rs4646605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4646606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4646607	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4646609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4646623	0.83[ASN][1000 genomes]
rs4646625	0.95[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4646626	0.95[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4646642	0.94[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs57975858	0.91[ASN][1000 genomes]
rs6493977	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs6493978	0.97[ASN][1000 genomes]
rs6493980	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6493981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs66971399	0.97[ASN][1000 genomes]
rs7171261	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7171714	0.94[ASN][1000 genomes]
rs7178598	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[ASN][1000 genomes]
rs7180059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8023769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8026952	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8027188	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8027964	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8032572	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8041644	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9635346	0.95[ASN][1000 genomes]
rs9635350	0.95[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	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
5	nsv569594	chr15:58336218-58347260	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6493979	PYGO1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58332200-58338200	Weak transcription	Fetal Intestine Large	intestine
2	chr15:58333800-58338200	Weak transcription	Fetal Intestine Small	intestine
3	chr15:58335800-58338200	Weak transcription	Fetal Kidney	kidney
4	chr15:58336000-58338200	Weak transcription	K562	blood
5	chr15:58336200-58338400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:58336400-58338600	Weak transcription	Fetal Lung	lung
7	chr15:58336400-58338800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr15:58336800-58338200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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