Variant report

Variant	rs12502204
Chromosome Location	chr4:186806447-186806448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:186779937..186782349-chr4:186806139..186807830,2	K562	blood:
2	chr4:186799508..186801311-chr4:186806279..186808668,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10020233	0.82[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap]
rs10031442	0.82[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs1026361	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1026362	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1031506	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11132357	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11132358	0.95[CEU][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11132359	0.87[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11132360	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11132361	0.81[ASN][1000 genomes]
rs11721899	0.90[ASW][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11722545	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11723186	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs11725663	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11725739	0.90[ASW][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11727209	0.80[ASN][1000 genomes]
rs11734074	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12503031	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504077	0.87[ASN][1000 genomes]
rs12508170	0.80[AFR][1000 genomes]
rs12640736	0.89[ASN][1000 genomes]
rs12643549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643665	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13110782	0.85[CHD][hapmap]
rs13114501	0.94[ASN][1000 genomes]
rs13120232	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs13132627	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs13138996	0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs13139354	0.94[ASN][1000 genomes]
rs13144263	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs13144444	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13150309	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1566354	0.82[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap]
rs1947455	0.82[MEX][hapmap]
rs2124092	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs2168165	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2310372	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs34067321	0.81[ASN][1000 genomes]
rs34122211	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34457125	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34458168	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34520754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34712366	0.89[ASN][1000 genomes]
rs34764127	0.81[ASN][1000 genomes]
rs34977118	0.81[ASN][1000 genomes]
rs35173472	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35318302	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35504695	0.81[ASN][1000 genomes]
rs35578127	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35820308	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35834071	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36076360	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4343763	0.83[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs4861687	0.94[ASN][1000 genomes]
rs4861688	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4862581	0.82[ASN][1000 genomes]
rs4862582	0.81[ASN][1000 genomes]
rs4862583	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4862584	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4862586	0.86[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs4862588	0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs55737156	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55926227	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55982043	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55990211	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs56086066	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs56122940	0.83[ASN][1000 genomes]
rs56130639	0.86[ASN][1000 genomes]
rs56218413	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56370835	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs56977523	0.86[ASN][1000 genomes]
rs62334984	0.83[ASN][1000 genomes]
rs62335022	0.86[ASN][1000 genomes]
rs6552934	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs6825889	0.90[ASN][1000 genomes]
rs6830105	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6853037	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs72707664	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7692862	0.82[CHB][hapmap];0.87[JPT][hapmap]

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	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1023917	chr4:186533075-186997806	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	7 gene(s)	inside rSNPs	diseases
3	nsv537420	chr4:186533075-186997806	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv530178	chr4:186659940-187478310	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
5	nsv1015236	chr4:186696172-187004074	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022661	chr4:186789827-187122464	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv537422	chr4:186789827-187122464	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12502204	ODZ3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:186802200-186811600	Weak transcription	Pancreas	Pancrea
2	chr4:186804000-186818000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:186805000-186814400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:186806400-186807400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr4:186806400-186815000	Weak transcription	Fetal Brain Female	brain

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