Variant report

Variant	rs12592900
Chromosome Location	chr15:54903895-54903896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10220855	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11071093	0.82[CHD][hapmap]
rs11632253	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11632366	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11852668	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11852743	0.92[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11856235	0.86[JPT][hapmap]
rs12592914	0.92[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12708436	0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1356857	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1520411	0.92[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1818704	0.84[CEU][hapmap]
rs1818711	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1850994	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1851000	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1851005	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1851010	0.92[CEU][hapmap]
rs1972137	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2414327	0.84[CEU][hapmap]
rs2414331	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2414332	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2460605	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2460606	0.96[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2553216	0.85[EUR][1000 genomes]
rs2553217	0.85[EUR][1000 genomes]
rs2553220	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2553221	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2553225	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2681959	0.85[EUR][1000 genomes]
rs2681964	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681965	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2681966	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2911846	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2911847	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2947001	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3848141	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3959676	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493694	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493695	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9284299	0.96[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1038660	chr15:54756184-55039913	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv904236	chr15:54820897-54912439	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1039548	chr15:54856965-54914519	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv569508	chr15:54876212-54904782	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv526413	chr15:54876423-54904782	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv904237	chr15:54888537-54927484	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv569509	chr15:54888537-54932716	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv457154	chr15:54892583-54904782	Weak transcription Enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv569517	chr15:54892583-54904782	Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv569518	chr15:54898631-54954864	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12592900	FGF7	cis	cerebellum	SCAN
rs12592900	XPC	cis	Cerebellum	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54900000-54920600	Weak transcription	Aorta	Aorta

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