Variant report

Variant	rs9889065
Chromosome Location	chr16:48512109-48512110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1001872	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1004704	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11076569	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11641936	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11643514	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11644887	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11648225	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11865776	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13333402	0.80[EUR][1000 genomes]
rs1566466	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1566467	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1948713	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2062553	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2062554	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2062555	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088753	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2088754	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4028695	0.85[CEU][hapmap]
rs4583237	0.81[EUR][1000 genomes]
rs4785244	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4785520	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4785521	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55745119	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56207849	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7184700	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7194822	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7198215	0.91[ASN][1000 genomes]
rs7198420	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7202699	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7203475	0.91[ASN][1000 genomes]
rs7206781	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8046716	0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs8052026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8054389	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8054696	0.91[ASN][1000 genomes]
rs8056201	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8056346	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8063059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9888862	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889067	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921402	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9923092	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9925108	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9926683	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9933892	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9937129	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9939368	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9939554	0.87[EUR][1000 genomes]
rs9940599	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9941289	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv1800739	chr16:48418505-48560315	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv428658	chr16:48438656-48587750	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv1833696	chr16:48504364-48512981	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
5	nsv511575	chr16:48504364-48512981	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
6	esv3312503	chr16:48506951-48512949	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	n/a
7	esv3312502	chr16:48507976-48512824	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	n/a
8	esv2652423	chr16:48508681-48512467	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	inside rSNPs	n/a
9	esv1792844	chr16:48509311-48512981	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	inside rSNPs	n/a
10	esv1815414	chr16:48509311-48512981	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	inside rSNPs	n/a
11	esv1848877	chr16:48509311-48512981	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	n/a
12	nsv572564	chr16:48509311-48512981	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
13	nsv572565	chr16:48509311-48519190	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a
14	esv1817281	chr16:48509311-48537421	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv1842977	chr16:48509311-48537421	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv1849228	chr16:48509311-48537421	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9889065	NKD1	cis	cerebellum	SCAN
rs9889065	N4BP1	cis	multi-tissue	Pritchard
rs9889065	NOD2	cis	cerebellum	SCAN
rs9889065	PAPD5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48508200-48512800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr16:48512000-48513600	Enhancers	Placenta	Placenta
3	chr16:48512000-48514000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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