Variant report

Variant	rs9921402
Chromosome Location	chr16:48526994-48526995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr16:48526744-48527045	A549	lung:	n/a	chr16:48526961-48526987
2	NR3C1	chr16:48526682-48527110	A549	lung:	n/a	chr16:48526961-48526987
3	USF1	chr16:48526841-48527140	A549	lung:	n/a	n/a
4	NR3C1	chr16:48526736-48527173	A549	lung:	n/a	chr16:48526961-48526987
5	FOXA1	chr16:48526746-48527247	A549	lung:	n/a	chr16:48527141-48527156
6	NR3C1	chr16:48526597-48527164	A549	lung:	n/a	chr16:48526961-48526987
7	NR3C1	chr16:48526735-48527148	A549	lung:	n/a	chr16:48526961-48526987
8	NR3C1	chr16:48526735-48527114	A549	lung:	n/a	chr16:48526961-48526987
9	FOXA1	chr16:48526703-48527342	A549	lung:	n/a	chr16:48527141-48527156
10	USF1	chr16:48526781-48527205	A549	lung:	n/a	n/a

Variant related genes	Relation type
MOCS1P1	TF binding region
ENSG00000239013	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1001872	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1004704	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11076569	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11641936	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11643514	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11644887	0.80[ASN][1000 genomes]
rs11648225	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11865776	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1566466	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1566467	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1948713	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2062553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062554	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2062555	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2088753	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2088754	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4028695	0.85[CEU][hapmap]
rs4785244	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4785520	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4785521	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55745119	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56207849	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6500390	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7184700	1.00[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs7189631	0.86[EUR][1000 genomes]
rs7194822	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7198215	0.82[ASN][1000 genomes]
rs7198420	1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7202699	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7203475	0.82[ASN][1000 genomes]
rs7206781	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8046716	0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs8052026	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054389	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8054696	0.82[ASN][1000 genomes]
rs8056201	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056346	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8057027	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8063059	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888862	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9889065	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9889067	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9923092	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9925108	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9925138	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9926683	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9933892	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9937129	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9939368	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9939554	0.87[EUR][1000 genomes]
rs9940599	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9941289	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	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	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
5	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
6	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
7	nsv1065358	chr16:48513824-48554254	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9921402	N4BP1	cis	multi-tissue	Pritchard
rs9921402	NKD1	cis	cerebellum	SCAN
rs9921402	NOD2	cis	cerebellum	SCAN
rs9921402	PAPD5	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48525000-48527000	Enhancers	Placenta	Placenta
2	chr16:48525400-48528400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr16:48525400-48532200	Weak transcription	Right Atrium	heart
4	chr16:48526200-48529400	Weak transcription	Fetal Stomach	stomach
5	chr16:48526400-48533000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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