Variant report

Variant	rs1520411
Chromosome Location	chr15:54919047-54919048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10220855	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11632253	0.88[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs11632366	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11852668	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852743	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856235	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12592900	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]
rs12592914	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs12708436	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs1356857	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1818711	0.88[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1850994	0.84[CEU][hapmap]
rs1851000	0.88[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]
rs1851005	0.87[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap]
rs1851010	0.84[CEU][hapmap]
rs1972137	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs2414331	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2414332	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2460605	0.88[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2460606	0.88[CEU][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs2460608	0.84[EUR][1000 genomes]
rs2553220	0.83[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2553221	0.87[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2553225	0.87[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2681964	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2681965	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681966	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2911846	0.83[ASN][1000 genomes]
rs2911847	0.88[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs2947001	0.88[CEU][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2947003	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3848141	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3959676	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493694	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493695	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9284299	0.88[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	nsv1043600	chr15:54910593-55010156	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
7	nsv1043237	chr15:54916301-55034633	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1520411	XPC	cis	Cerebellum	GTEx
rs1520411	MYO5C	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54900000-54920600	Weak transcription	Aorta	Aorta
2	chr15:54918000-54920400	Weak transcription	Fetal Lung	lung

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