Variant report

Variant	rs12118732
Chromosome Location	chr1:212454914-212454915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:212454875-212455322	IMR90	lung:	n/a	chr1:212455125-212455136
2	CEBPB	chr1:212454913-212455300	Hela-S3	cervix:	n/a	chr1:212455125-212455136

Variant related genes	Relation type
PPP2R5A	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1056985	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10863956	1.00[AFR][1000 genomes]
rs11119886	1.00[AFR][1000 genomes]
rs11119891	1.00[AFR][1000 genomes]
rs11119893	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11119903	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11119907	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119908	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11119910	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11119918	0.84[ASN][1000 genomes]
rs12118709	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12124582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12128123	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12128965	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12129267	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12133636	0.84[ASN][1000 genomes]
rs12134074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134599	0.83[ASN][1000 genomes]
rs12136095	0.83[ASN][1000 genomes]
rs12137798	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12138533	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12140158	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12143853	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12145170	0.83[ASN][1000 genomes]
rs12145377	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12145484	0.83[ASN][1000 genomes]
rs12146141	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12561785	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12562618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1342152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs14123	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1493601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17018847	0.85[AMR][1000 genomes]
rs17018853	0.85[AMR][1000 genomes]
rs2236598	0.98[ASN][1000 genomes]
rs2298115	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61260530	0.81[AMR][1000 genomes]
rs903119	1.00[AFR][1000 genomes];0.85[AMR][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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv1799093	chr1:212447167-212468974	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1800932	chr1:212447167-212468974	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv1839997	chr1:212447167-212468974	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12118732	PPP2R5A	cis	Thyroid	GTEx
rs12118732	PPP2R5A	cis	Whole Blood	GTEx
rs12118732	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212446000-212457000	Weak transcription	Stomach Mucosa	stomach
2	chr1:212446000-212457600	Weak transcription	Fetal Brain Female	brain
3	chr1:212446400-212457200	Weak transcription	Fetal Heart	heart
4	chr1:212454200-212457200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:212454600-212455400	Enhancers	Fetal Lung	lung

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