Variant report

Variant	rs2476588
Chromosome Location	chr9:9779358-9779359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10816178	0.89[ASN][1000 genomes]
rs10816180	0.80[ASN][1000 genomes]
rs10977967	0.85[ASN][1000 genomes]
rs10977976	0.89[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap]
rs1323800	0.86[YRI][hapmap]
rs1629016	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1746793	0.89[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1768878	0.89[CHB][hapmap]
rs1768883	0.85[ASN][1000 genomes]
rs2147066	0.96[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2147067	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2181715	0.92[EUR][1000 genomes]
rs2244516	0.83[CHB][hapmap]
rs2382054	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2382055	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2382056	0.83[CHB][hapmap]
rs2476587	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2476589	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2494403	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2761717	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2761718	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2761720	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2761722	0.82[EUR][1000 genomes]
rs2761723	0.82[ASW][hapmap];0.88[CEU][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2761724	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2761727	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2821470	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2821472	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2821473	0.89[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2821492	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2821493	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2821494	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2821495	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2821496	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2821497	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2821498	1.00[ASW][hapmap];0.87[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2821499	0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2821500	0.89[ASN][1000 genomes]
rs2821501	0.89[ASN][1000 genomes]
rs2821502	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2821507	0.88[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3122699	0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7048068	0.82[YRI][hapmap]
rs768224	0.84[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs768225	0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7863452	0.90[YRI][hapmap]
rs7874425	0.83[CHB][hapmap];0.86[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892264	chr9:9440838-9796577	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv892265	chr9:9476425-9796116	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv892270	chr9:9591059-9860735	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1028772	chr9:9631694-9779358	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2422381	chr9:9647540-9887820	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1020468	chr9:9658670-9780975	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv539983	chr9:9658670-9780975	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv892274	chr9:9687742-9787587	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv526471	chr9:9718066-9832245	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1034236	chr9:9728895-9779358	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2829906	chr9:9737201-9897866	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv2753276	chr9:9762533-9799050	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv892275	chr9:9763352-9794545	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1033299	chr9:9776126-9796116	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1034731	chr9:9776126-10481262	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv892276	chr9:9778653-9851382	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv2753179	chr9:9778653-9861006	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2476588	KDM4C	cis	cerebellum	SCAN
rs2476588	TPD52L3	cis	cerebellum	SCAN
rs2476588	RPL22L1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:9779000-9782000	Weak transcription	HUVEC	blood vessel

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