Variant report

Variant	rs927744
Chromosome Location	chr1:216096763-216096764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:216074148..216076361-chr1:216095945..216097461,2	K562	blood:
2	chr1:216096007..216097602-chr1:216102909..216104779,2	K562	blood:
3	chr1:216095323..216098223-chr1:216099775..216101412,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10746460	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.92[TSI][hapmap]
rs12140657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1575756	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1934424	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs2576002	0.90[CHB][hapmap]
rs2764947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2764951	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4564111	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.99[ASN][1000 genomes]
rs479826	0.90[CHB][hapmap]
rs489857	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs492474	0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs494350	0.89[ASN][1000 genomes]
rs498911	0.82[ASW][hapmap];0.82[TSI][hapmap]
rs513746	0.82[TSI][hapmap]
rs517577	0.81[AMR][1000 genomes]
rs519859	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs531780	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs542423	0.90[CHB][hapmap]
rs547022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs553986	0.89[ASN][1000 genomes]
rs559921	0.82[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs646576	0.81[AMR][1000 genomes]
rs647908	0.81[AMR][1000 genomes]
rs654702	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs662355	0.81[AMR][1000 genomes]
rs687019	0.90[CHB][hapmap]
rs687693	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7544470	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs772713	0.81[TSI][hapmap]

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	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949671	chr1:215942740-216120815	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv832548	chr1:215987089-216175724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv428599	chr1:216086224-216267211	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs927744	USH2A	cis	parietal	SCAN
rs927744	RD3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216096400-216097000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:216096600-216097000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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