Variant report

Variant	rs55782524
Chromosome Location	chr16:48557493-48557494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:48417609..48422377-chr16:48557462..48561956,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196470	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs1039340	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1039341	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1039342	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1039343	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1039344	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1106386	0.92[EUR][1000 genomes]
rs11076570	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11076571	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11076572	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11076573	0.88[EUR][1000 genomes]
rs11076578	0.83[EUR][1000 genomes]
rs1115758	0.92[EUR][1000 genomes]
rs1115759	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1120275	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1120276	0.92[EUR][1000 genomes]
rs11495819	0.84[EUR][1000 genomes]
rs11640463	0.87[EUR][1000 genomes]
rs11641458	0.86[EUR][1000 genomes]
rs11643264	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643272	0.87[EUR][1000 genomes]
rs11644518	0.91[EUR][1000 genomes]
rs11645193	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11647046	0.90[EUR][1000 genomes]
rs11647048	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11648101	0.83[EUR][1000 genomes]
rs11649236	0.88[EUR][1000 genomes]
rs11859909	0.87[EUR][1000 genomes]
rs1224	0.93[EUR][1000 genomes]
rs12446280	0.86[EUR][1000 genomes]
rs12597928	0.83[EUR][1000 genomes]
rs12598514	0.83[EUR][1000 genomes]
rs12933948	0.84[EUR][1000 genomes]
rs12935540	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13331902	0.85[EUR][1000 genomes]
rs1386040	0.88[EUR][1000 genomes]
rs1386042	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1477134	0.83[EUR][1000 genomes]
rs1486411	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1486412	0.87[EUR][1000 genomes]
rs1564979	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16946342	0.87[EUR][1000 genomes]
rs17826468	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1825683	0.87[EUR][1000 genomes]
rs1872652	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1872654	0.86[EUR][1000 genomes]
rs1872655	0.86[EUR][1000 genomes]
rs1909765	0.91[EUR][1000 genomes]
rs1987061	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2041921	0.83[EUR][1000 genomes]
rs2080507	0.82[EUR][1000 genomes]
rs2080508	0.84[EUR][1000 genomes]
rs2101372	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2129243	0.86[EUR][1000 genomes]
rs2354578	0.92[EUR][1000 genomes]
rs2354579	0.92[EUR][1000 genomes]
rs28449353	1.00[ASN][1000 genomes]
rs28577888	0.83[EUR][1000 genomes]
rs2883475	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36077931	0.92[EUR][1000 genomes]
rs3743779	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3743780	0.87[EUR][1000 genomes]
rs3817029	0.92[EUR][1000 genomes]
rs3826174	0.92[EUR][1000 genomes]
rs3843724	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3848319	0.92[EUR][1000 genomes]
rs3848320	0.84[EUR][1000 genomes]
rs3848321	0.89[EUR][1000 genomes]
rs3848322	0.91[EUR][1000 genomes]
rs4493038	0.84[EUR][1000 genomes]
rs4785247	0.85[EUR][1000 genomes]
rs4785248	0.85[EUR][1000 genomes]
rs4785528	0.85[EUR][1000 genomes]
rs55671623	0.88[EUR][1000 genomes]
rs6500395	0.91[EUR][1000 genomes]
rs6500396	0.89[EUR][1000 genomes]
rs6500397	0.86[EUR][1000 genomes]
rs6500398	0.87[EUR][1000 genomes]
rs6500405	0.84[EUR][1000 genomes]
rs7184070	0.85[EUR][1000 genomes]
rs7184144	0.90[EUR][1000 genomes]
rs7185899	0.81[EUR][1000 genomes]
rs7187513	0.92[EUR][1000 genomes]
rs7188741	0.92[EUR][1000 genomes]
rs7191028	0.91[EUR][1000 genomes]
rs7192297	0.85[EUR][1000 genomes]
rs7194570	0.85[EUR][1000 genomes]
rs7195684	0.83[EUR][1000 genomes]
rs7196823	0.90[EUR][1000 genomes]
rs7197732	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7198773	0.90[EUR][1000 genomes]
rs7199206	0.84[EUR][1000 genomes]
rs7199625	0.88[EUR][1000 genomes]
rs7201196	0.85[EUR][1000 genomes]
rs8044519	0.87[EUR][1000 genomes]
rs8052073	0.84[EUR][1000 genomes]
rs8052640	0.91[EUR][1000 genomes]
rs8053598	0.87[EUR][1000 genomes]
rs8057165	0.90[EUR][1000 genomes]
rs8057777	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8058362	0.87[EUR][1000 genomes]
rs8059819	0.83[EUR][1000 genomes]
rs8059905	0.87[EUR][1000 genomes]
rs868792	0.87[EUR][1000 genomes]
rs871902	0.92[EUR][1000 genomes]
rs924476	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989070	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9921737	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9921741	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9922356	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9922734	0.92[EUR][1000 genomes]
rs9923371	0.88[EUR][1000 genomes]
rs9923753	0.83[EUR][1000 genomes]
rs9924078	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924483	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9925108	0.81[AFR][1000 genomes]
rs9925406	0.86[EUR][1000 genomes]
rs9927888	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928051	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930199	0.93[EUR][1000 genomes]
rs9930644	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9931123	0.91[EUR][1000 genomes]
rs9931737	0.90[EUR][1000 genomes]
rs9933187	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933329	0.85[EUR][1000 genomes]
rs9933976	0.92[EUR][1000 genomes]
rs9934626	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9934844	0.86[EUR][1000 genomes]
rs9936004	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9936271	0.90[EUR][1000 genomes]
rs9936445	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9936446	0.88[EUR][1000 genomes]
rs9936454	0.91[EUR][1000 genomes]
rs9937134	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9937568	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9937610	0.86[EUR][1000 genomes]
rs9937623	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9938126	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9938308	0.91[EUR][1000 genomes]
rs9938890	0.90[EUR][1000 genomes]
rs9939103	0.92[EUR][1000 genomes]
rs9941275	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9941336	0.86[EUR][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	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	nsv1064323	chr16:48531171-48573066	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1060196	chr16:48531171-48578101	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55782524	N4BP1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48555800-48558000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:48555800-48561000	Enhancers	Placenta	Placenta
3	chr16:48556800-48558200	Bivalent Enhancer	HepG2	liver
4	chr16:48557400-48559800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr16:48557400-48560000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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