Variant report

Variant	rs12046356
Chromosome Location	chr1:216076167-216076168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:216074148..216076361-chr1:216095945..216097461,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10495012	0.87[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap]
rs10864214	0.86[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10864215	0.87[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11120694	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120697	0.87[CHB][hapmap];0.84[JPT][hapmap];0.98[ASN][1000 genomes]
rs11120698	0.94[ASW][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11120699	0.87[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap]
rs12034100	0.84[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12090189	0.81[AFR][1000 genomes]
rs12091359	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs12562080	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1836937	0.81[ASN][1000 genomes]
rs1934423	0.82[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365632	0.94[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3908469	0.87[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4655288	1.00[YRI][hapmap]
rs4655433	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6661521	1.00[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs6665202	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap]
rs6675583	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs942838	1.00[YRI][hapmap];0.80[AFR][1000 genomes]

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	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12046356	NEK2	cis	parietal	SCAN
rs12046356	USH2A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216075400-216076200	Enhancers	Pancreatic Islets	Pancreatic Islet

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