Variant report

Variant	rs16999566
Chromosome Location	chr4:167003769-167003770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10011050	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11729467	0.81[EUR][1000 genomes]
rs11730398	0.92[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs11730477	0.80[EUR][1000 genomes]
rs12648178	0.94[ASN][1000 genomes]
rs12650522	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs1503302	0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1503303	0.92[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs2173307	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2202252	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2292082	1.00[CEU][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2292083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28366617	0.86[ASN][1000 genomes]
rs28380606	0.81[EUR][1000 genomes]
rs28636651	0.89[ASN][1000 genomes]
rs3756016	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs3756017	0.80[EUR][1000 genomes]
rs4388044	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4429697	0.82[EUR][1000 genomes]
rs55639375	0.87[ASN][1000 genomes]
rs6536940	0.81[EUR][1000 genomes]
rs6536943	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6536944	0.83[EUR][1000 genomes]
rs6536945	0.85[EUR][1000 genomes]
rs66538513	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6815812	0.82[EUR][1000 genomes]
rs6823990	0.86[EUR][1000 genomes]
rs6857845	0.83[EUR][1000 genomes]
rs72697388	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7664119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7671123	0.85[EUR][1000 genomes]
rs7678997	0.86[EUR][1000 genomes]
rs7684252	0.96[CEU][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7686255	0.85[EUR][1000 genomes]
rs7693478	0.92[CEU][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs7694649	0.92[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	nsv821638	chr4:166837633-167262625	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv830142	chr4:166935555-167095922	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1034421	chr4:166961339-167893289	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537339	chr4:166961339-167893289	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3323263	chr4:167002302-167006800	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
6	nsv513176	chr4:167002722-167005568	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
7	esv3510223	chr4:167003577-167005950	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16999566	NEK1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166987000-167004800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:166993800-167004000	Weak transcription	Pancreas	Pancrea
3	chr4:167003400-167007600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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