Variant report

Variant	rs2899611
Chromosome Location	chr15:58327347-58327348
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	chr15:58325674..58328076-chr15:58330159..58331775,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10518961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1061278	0.95[CHB][hapmap]
rs1063666	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs10851630	0.86[YRI][hapmap]
rs10851632	0.94[CHB][hapmap]
rs11071363	0.97[ASN][1000 genomes]
rs11071364	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11071367	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11629553	0.87[ASN][1000 genomes]
rs11629583	0.94[ASN][1000 genomes]
rs11631127	0.91[ASN][1000 genomes]
rs11636979	0.94[ASN][1000 genomes]
rs11855259	0.86[YRI][hapmap]
rs11857465	0.99[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];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12595180	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs12595410	0.98[ASN][1000 genomes]
rs12898976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][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	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12909865	0.98[ASN][1000 genomes]
rs12909979	0.84[ASN][1000 genomes]
rs12911450	0.98[ASN][1000 genomes]
rs12912093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12914388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12914414	0.98[ASN][1000 genomes]
rs12914455	0.95[ASN][1000 genomes]
rs12914603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12915508	0.94[ASN][1000 genomes]
rs12915821	0.97[ASN][1000 genomes]
rs12915989	0.97[ASN][1000 genomes]
rs12917536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1372369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1441815	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1441819	0.95[CHB][hapmap]
rs1441829	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[YRI][hapmap];0.94[ASN][1000 genomes]
rs17820966	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17820990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1812889	0.84[ASN][1000 genomes]
rs1822205	1.00[CHB][hapmap];0.95[CHD][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];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1994926	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1994927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2044071	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2067062	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2119859	0.87[AFR][1000 genomes]
rs2197092	0.95[CHB][hapmap]
rs2414527	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2414529	0.98[ASN][1000 genomes]
rs2414530	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2642630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2642632	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2704196	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2704197	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704218	0.81[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs2704225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2899612	0.96[ASN][1000 genomes]
rs2899613	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3204689	0.86[YRI][hapmap]
rs3204690	0.95[CHB][hapmap]
rs33960206	0.95[ASN][1000 genomes]
rs34226780	0.98[ASN][1000 genomes]
rs34556514	0.97[ASN][1000 genomes]
rs34676542	0.98[ASN][1000 genomes]
rs34958088	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742959	0.95[CHB][hapmap];0.83[CHD][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];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3784259	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3784262	0.84[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs3784264	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3809535	0.87[ASN][1000 genomes]
rs4144005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4238327	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4553566	0.96[ASN][1000 genomes]
rs4646549	0.88[ASN][1000 genomes]
rs4646554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4646555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4646557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4646559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4646560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4646564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4646566	0.95[ASN][1000 genomes]
rs4646570	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646572	0.86[YRI][hapmap];0.82[AFR][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];0.91[YRI][hapmap];0.84[AFR][1000 genomes];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];0.96[ASN][1000 genomes]
rs4646590	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4646592	0.96[ASN][1000 genomes]
rs4646594	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4646595	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[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];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs4646602	0.98[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];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4646609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4646623	0.86[ASN][1000 genomes]
rs4646625	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4646626	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4646638	0.95[YRI][hapmap]
rs4646640	0.86[YRI][hapmap]
rs4646642	0.94[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs57975858	0.91[ASN][1000 genomes]
rs6493977	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6493978	1.00[ASN][1000 genomes]
rs6493979	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6493980	0.92[ASN][1000 genomes]
rs6493981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs66971399	1.00[ASN][1000 genomes]
rs7165247	0.84[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7170896	0.86[AFR][1000 genomes]
rs7171261	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7171714	0.98[ASN][1000 genomes]
rs7178598	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7180059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7495968	0.81[YRI][hapmap]
rs8023769	0.96[ASN][1000 genomes]
rs8026952	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8027188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8027964	0.96[ASN][1000 genomes]
rs8032572	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs8041644	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9325	0.86[YRI][hapmap]
rs9635346	0.95[ASN][1000 genomes]
rs9635350	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2899611	PYGO1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58325200-58328400	Weak transcription	Fetal Kidney	kidney
2	chr15:58325400-58329200	Weak transcription	K562	blood
3	chr15:58326800-58327400	Enhancers	NHEK	skin
4	chr15:58327200-58327400	Active TSS	Psoas Muscle	Psoas
5	chr15:58327200-58330400	Weak transcription	HMEC	breast

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