Variant report

Variant	rs804889
Chromosome Location	chr16:81096539-81096540
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81096522..81104265-chr16:81107324..81112531,10	MCF-7	breast:
2	chr16:81069323..81071129-chr16:81095965..81099347,3	MCF-7	breast:
3	chr16:81093322..81097410-chr16:81102754..81106923,4	MCF-7	breast:
4	chr16:81083129..81085319-chr16:81095819..81098738,2	K562	blood:
5	chr16:81091735..81094640-chr16:81096464..81099185,2	K562	blood:
6	chr16:81094141..81096818-chr16:81110183..81111758,2	K562	blood:

Variant related genes	Relation type
ENSG00000260213	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000261838	Chromatin interaction
ENSG00000166454	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1035541	0.87[ASN][1000 genomes]
rs10459871	0.93[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs10459872	0.93[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs1050364	0.93[ASN][1000 genomes]
rs10514512	0.81[ASN][1000 genomes]
rs10514513	0.85[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs10514514	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10514515	0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs11537	0.93[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs12443549	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs12444137	0.82[ASN][1000 genomes]
rs12444969	0.85[ASN][1000 genomes]
rs12445303	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12598621	0.88[ASN][1000 genomes]
rs1410	0.91[ASN][1000 genomes]
rs1412	0.92[ASN][1000 genomes]
rs1414	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1563075	0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs1563077	0.94[ASN][1000 genomes]
rs16954572	0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs16954582	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1965237	0.88[ASN][1000 genomes]
rs2278022	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs2278024	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs2287995	0.87[ASN][1000 genomes]
rs2549891	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs28391685	0.93[ASN][1000 genomes]
rs28613188	0.93[ASN][1000 genomes]
rs28672349	0.93[ASN][1000 genomes]
rs4306521	0.93[ASN][1000 genomes]
rs4324141	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4324142	0.93[ASN][1000 genomes]
rs4324143	0.92[ASN][1000 genomes]
rs4889227	0.94[ASN][1000 genomes]
rs4889231	0.93[ASN][1000 genomes]
rs55939311	0.82[ASN][1000 genomes]
rs56032321	0.93[ASN][1000 genomes]
rs56119129	0.93[ASN][1000 genomes]
rs56166222	0.83[ASN][1000 genomes]
rs56395947	0.93[ASN][1000 genomes]
rs58144189	0.87[ASN][1000 genomes]
rs59177227	0.93[ASN][1000 genomes]
rs59685942	0.93[ASN][1000 genomes]
rs62054594	0.80[ASN][1000 genomes]
rs7188508	0.93[ASN][1000 genomes]
rs7204040	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs754429	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs804895	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs804896	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs804897	0.95[ASN][1000 genomes]
rs804902	0.86[CHB][hapmap]
rs804903	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs804904	0.81[GIH][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs804905	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8052490	0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs8056972	0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs8177939	0.91[ASN][1000 genomes]
rs8177940	0.85[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs8177942	0.81[ASN][1000 genomes]
rs8177943	0.93[ASN][1000 genomes]
rs8177945	0.93[ASN][1000 genomes]
rs8177948	0.93[ASN][1000 genomes]
rs8177950	0.93[ASN][1000 genomes]
rs8177957	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs8177959	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9806918	0.86[ASN][1000 genomes]
rs9923732	0.84[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs9925940	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9925943	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9926174	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9929586	0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9933184	0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9938965	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
6	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1897	chr16:81060566-81105260	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	esv2751615	chr16:81093099-81307599	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs804889	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs804889	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81079400-81109800	Weak transcription	Brain Hippocampus Middle	brain
2	chr16:81080400-81110200	Weak transcription	Ovary	ovary
3	chr16:81083800-81099800	Weak transcription	Brain Angular Gyrus	brain
4	chr16:81090200-81097600	Weak transcription	Pancreas	Pancrea
5	chr16:81092000-81106600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:81093000-81109800	Weak transcription	Brain Anterior Caudate	brain
7	chr16:81093200-81100200	Weak transcription	Brain Germinal Matrix	brain
8	chr16:81093600-81100000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr16:81094600-81098000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr16:81095000-81109400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr16:81095600-81097200	Weak transcription	Placenta	Placenta
12	chr16:81095600-81101000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr16:81095600-81109800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr16:81095800-81110200	Weak transcription	Fetal Stomach	stomach

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