Variant report

Variant	rs2883475
Chromosome Location	chr16:48560315-48560316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:48559845..48562587-chr16:48571698..48574105,2	K562	blood:
2	chr16:48393689..48396350-chr16:48558583..48560926,2	MCF-7	breast:
3	chr16:48387226..48388138-chr16:48560079..48561124,3	MCF-7	breast:
4	chr16:48267927..48268788-chr16:48560181..48561094,2	MCF-7	breast:
5	chr16:48560129..48561061-chr16:48657041..48657742,3	MCF-7	breast:
6	chr16:48417609..48422377-chr16:48557462..48561956,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260086	Chromatin interaction
ENSG00000196470	Chromatin interaction

Extended variants
information (count: 152 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs1039340	1.00[CEU][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1039341	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1039342	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1039343	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1039344	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1106386	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11076570	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11076571	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11076572	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs11076573	0.89[EUR][1000 genomes]
rs11076578	0.84[EUR][1000 genomes]
rs1115758	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1115759	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1120275	0.96[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1120276	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11495819	0.85[EUR][1000 genomes]
rs11640463	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11641458	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs11643264	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643272	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11644518	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11645193	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11647046	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs11647048	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11648101	0.83[EUR][1000 genomes]
rs11649236	1.00[CEU][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11859909	0.89[EUR][1000 genomes]
rs1224	1.00[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12446280	0.86[EUR][1000 genomes]
rs12597928	0.84[EUR][1000 genomes]
rs12598514	0.85[EUR][1000 genomes]
rs12933948	0.85[EUR][1000 genomes]
rs12935540	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13331902	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1386040	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1386042	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1477134	0.84[EUR][1000 genomes]
rs1486411	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1486412	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1558815	0.81[EUR][1000 genomes]
rs1564979	0.96[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16946340	0.82[CHB][hapmap]
rs16946342	0.88[EUR][1000 genomes]
rs17826468	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1825683	0.88[EUR][1000 genomes]
rs1872652	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1872654	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs1872655	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs1909765	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1987061	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2041921	0.84[EUR][1000 genomes]
rs2080507	0.83[EUR][1000 genomes]
rs2080508	0.85[EUR][1000 genomes]
rs2101372	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2129243	1.00[CEU][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2354578	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2354579	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28449353	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28577888	0.84[EUR][1000 genomes]
rs36077931	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3743779	1.00[CEU][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3743780	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3817029	1.00[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3826174	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3843724	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3848319	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3848320	0.84[EUR][1000 genomes]
rs3848321	0.90[EUR][1000 genomes]
rs3848322	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3859121	1.00[CHB][hapmap]
rs4493038	0.85[EUR][1000 genomes]
rs4785247	0.86[EUR][1000 genomes]
rs4785248	0.86[EUR][1000 genomes]
rs4785528	0.86[EUR][1000 genomes]
rs55671623	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55782524	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6500395	1.00[CEU][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6500396	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6500397	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6500398	0.88[EUR][1000 genomes]
rs6500405	0.85[EUR][1000 genomes]
rs7184070	0.86[EUR][1000 genomes]
rs7184144	0.92[EUR][1000 genomes]
rs7185899	0.82[EUR][1000 genomes]
rs7187513	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7188741	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7191028	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7191225	0.84[MEX][hapmap]
rs7192297	0.86[EUR][1000 genomes]
rs7194570	0.86[EUR][1000 genomes]
rs7195684	0.84[EUR][1000 genomes]
rs7196823	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7197732	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7198145	0.84[MEX][hapmap]
rs7198773	0.92[EUR][1000 genomes]
rs7199206	0.85[EUR][1000 genomes]
rs7199625	0.88[EUR][1000 genomes]
rs7201196	0.86[EUR][1000 genomes]
rs8044519	0.89[EUR][1000 genomes]
rs8052073	0.85[EUR][1000 genomes]
rs8052640	1.00[CEU][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8053598	0.89[EUR][1000 genomes]
rs8057165	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8057777	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8058362	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8059819	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs8059905	1.00[CEU][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs868792	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs871902	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs904818	1.00[CEU][hapmap]
rs924476	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989070	0.96[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9921737	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9921741	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9922356	0.96[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9922734	1.00[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9923371	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9923753	0.84[EUR][1000 genomes]
rs9924078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924483	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9925406	0.87[EUR][1000 genomes]
rs9927888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930199	1.00[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9930644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9931123	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9931737	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9933187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933329	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9933976	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9934626	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9934844	0.86[EUR][1000 genomes]
rs9936004	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9936271	0.91[EUR][1000 genomes]
rs9936445	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9936446	0.88[EUR][1000 genomes]
rs9936454	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9937134	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9937568	0.96[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9937610	0.87[EUR][1000 genomes]
rs9937623	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9938126	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9938308	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9938890	0.92[EUR][1000 genomes]
rs9939103	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9941275	1.00[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[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
rs2883475	N4BP1	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48555800-48561000	Enhancers	Placenta	Placenta
2	chr16:48558000-48561000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:48558200-48561000	Flanking Bivalent TSS/Enh	HepG2	liver
4	chr16:48558600-48561200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:48558800-48560400	Enhancers	Primary B cells from peripheral blood	blood
6	chr16:48559000-48561000	Enhancers	Colonic Mucosa	Colon
7	chr16:48559000-48561000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr16:48559200-48565600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr16:48559200-48571600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr16:48559400-48560400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr16:48559400-48561200	Enhancers	Stomach Mucosa	stomach
12	chr16:48559600-48570400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:48559800-48560600	Weak transcription	HMEC	breast
14	chr16:48559800-48560800	Weak transcription	Spleen	Spleen
15	chr16:48560000-48561000	Enhancers	Hela-S3	cervix
16	chr16:48560000-48561200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:48560000-48561200	Enhancers	NHEK	skin
18	chr16:48560200-48560400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr16:48560200-48560600	Flanking Active TSS	Liver	Liver
20	chr16:48560200-48560600	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr16:48560200-48560600	Flanking Active TSS	Fetal Intestine Large	intestine
22	chr16:48560200-48560600	Active TSS	Fetal Intestine Small	intestine
23	chr16:48560200-48560600	Enhancers	Pancreas	Pancrea
24	chr16:48560200-48560800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr16:48560200-48561000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr16:48560200-48561000	Enhancers	Esophagus	oesophagus
27	chr16:48560200-48561200	Enhancers	Skeletal Muscle Male	skeletal muscle

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