Variant report

Variant	rs6488878
Chromosome Location	chr12:124023932-124023933
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	chr12:124015786..124020200-chr12:124020787..124024805,6	K562	blood:
2	chr12:124014613..124020427-chr12:124021757..124030921,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1050443	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1050448	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1050449	0.89[ASN][1000 genomes]
rs11057297	0.94[CEU][hapmap]
rs11612927	1.00[JPT][hapmap]
rs11833889	0.89[ASN][1000 genomes]
rs12809853	1.00[JPT][hapmap]
rs1533246	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs15587	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2333832	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28492040	0.84[EUR][1000 genomes]
rs3190835	0.89[ASN][1000 genomes]
rs3204541	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs34097324	0.89[ASN][1000 genomes]
rs34514002	0.89[ASN][1000 genomes]
rs35016092	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35708602	0.89[ASN][1000 genomes]
rs35867744	0.89[ASN][1000 genomes]
rs36002329	0.89[ASN][1000 genomes]
rs4930737	1.00[JPT][hapmap]
rs55705511	0.89[ASN][1000 genomes]
rs56675602	0.89[ASN][1000 genomes]
rs59126974	0.89[ASN][1000 genomes]
rs6488877	0.90[EUR][1000 genomes]
rs66694750	0.89[ASN][1000 genomes]
rs68163141	0.89[ASN][1000 genomes]
rs7137473	0.89[ASN][1000 genomes]
rs7139162	0.89[ASN][1000 genomes]
rs71458807	0.89[ASN][1000 genomes]
rs7303956	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7308304	0.89[ASN][1000 genomes]
rs7959714	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963804	0.90[EUR][1000 genomes]
rs7974279	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6488878	PERP	trans	lymphoblastoid	seeQTL
rs6488878	DDX55	cis	parietal	SCAN
rs6488878	TCTN2	cis	parietal	SCAN
rs6488878	ANAPC5	cis	parietal	SCAN
rs6488878	TCTN2	cis	cerebellum	SCAN
rs6488878	DDX55	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124019400-124028200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:124023600-124024200	Enhancers	HepG2	liver

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