Variant report

Variant	rs7239486
Chromosome Location	chr18:12941772-12941773
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12939289..12942214-chr18:12945924..12948391,4	MCF-7	breast:
2	chr18:12939763..12942189-chr18:12946209..12948474,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085415	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10163827	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11080617	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11080618	0.89[ASN][1000 genomes]
rs11662634	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11662766	0.83[ASN][1000 genomes]
rs11664213	0.89[ASN][1000 genomes]
rs11664469	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12604538	0.85[ASN][1000 genomes]
rs12605267	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12607398	0.89[ASN][1000 genomes]
rs12607919	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12953783	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12957380	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12960349	0.89[ASN][1000 genomes]
rs12961596	0.90[ASN][1000 genomes]
rs12963426	0.88[ASN][1000 genomes]
rs12967249	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12970503	0.90[ASN][1000 genomes]
rs13381779	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17603207	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17659689	0.92[ASN][1000 genomes]
rs17659749	0.92[ASN][1000 genomes]
rs17659896	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2282541	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28551661	0.88[ASN][1000 genomes]
rs28654613	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34166083	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34302481	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34765181	0.85[ASN][1000 genomes]
rs35368962	0.93[ASN][1000 genomes]
rs35563947	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3809914	0.95[ASN][1000 genomes]
rs3976787	0.90[ASN][1000 genomes]
rs6505772	0.82[ASN][1000 genomes]
rs67768874	0.81[ASN][1000 genomes]
rs68004799	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7228684	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7229406	0.82[ASN][1000 genomes]
rs7230391	0.88[ASN][1000 genomes]
rs7234938	0.83[ASN][1000 genomes]
rs7236710	0.84[EUR][1000 genomes]
rs8083393	0.83[ASN][1000 genomes]
rs8083401	0.83[ASN][1000 genomes]
rs8086882	0.80[ASN][1000 genomes]
rs8089724	0.90[ASN][1000 genomes]
rs8090667	0.92[ASN][1000 genomes]
rs8093236	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8093576	0.92[ASN][1000 genomes]
rs8566	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9950241	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers 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	46 gene(s)	inside rSNPs	diseases
8	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	esv3450694	chr18:12933001-12955144	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7239486	CEP192	cis	lung	GTEx
rs7239486	CEP192	cis	Thyroid	GTEx
rs7239486	CEP192	cis	Esophagus Muscularis	GTEx
rs7239486	CEP192	cis	Artery Tibial	GTEx
rs7239486	CEP192	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12935000-12944600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr18:12938600-12946000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr18:12939600-12944800	Weak transcription	Dnd41	blood
4	chr18:12940000-12942800	Weak transcription	Fetal Thymus	thymus
5	chr18:12940200-12943000	Weak transcription	Thymus	Thymus

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