Variant report

Variant	rs786455
Chromosome Location	chr12:124054766-124054767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124041024..124043349-chr12:124054707..124057427,2	MCF-7	breast:
2	chr12:124017387..124020298-chr12:124054468..124057519,3	MCF-7	breast:
3	chr12:124054266..124056450-chr12:124065485..124066989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10082874	0.97[AMR][1000 genomes]
rs10846531	0.89[CEU][hapmap]
rs11057298	0.89[CEU][hapmap]
rs11057302	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs11057306	0.89[CEU][hapmap]
rs11522341	0.80[CEU][hapmap]
rs11535679	0.80[CEU][hapmap]
rs11615043	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11834369	0.80[EUR][1000 genomes]
rs11837236	0.80[EUR][1000 genomes]
rs12099981	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs12099986	0.80[EUR][1000 genomes]
rs1707722	1.00[YRI][hapmap]
rs1707723	1.00[YRI][hapmap]
rs1877365	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2048802	0.80[CEU][hapmap]
rs2340691	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs28493578	0.80[CEU][hapmap]
rs28673982	0.88[CEU][hapmap]
rs28691687	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28894691	0.80[CEU][hapmap]
rs3209852	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34099549	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3748268	0.80[CEU][hapmap]
rs4930715	0.84[EUR][1000 genomes]
rs61678733	0.80[EUR][1000 genomes]
rs6488879	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6488881	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs7136101	0.81[EUR][1000 genomes]
rs7301377	0.80[EUR][1000 genomes]
rs7303554	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7316613	0.82[EUR][1000 genomes]
rs73414262	0.80[EUR][1000 genomes]
rs786427	1.00[YRI][hapmap]
rs786428	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs786429	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs786431	0.80[EUR][1000 genomes]
rs786432	0.80[EUR][1000 genomes]
rs786434	0.80[EUR][1000 genomes]
rs786435	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs786438	0.80[EUR][1000 genomes]
rs786439	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs786440	1.00[YRI][hapmap]
rs786450	0.80[EUR][1000 genomes]
rs7954782	0.80[EUR][1000 genomes]
rs7958153	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7960812	0.80[EUR][1000 genomes]
rs7971779	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs884892	0.80[CEU][hapmap]
rs952360	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs9697379	1.00[CEU][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	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
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs786455	RP11-486O12.2	cis	Thyroid	GTEx
rs786455	DDX55	cis	Thyroid	GTEx
rs786455	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs786455	RP11-486O12.2	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124054200-124055400	Enhancers	Dnd41	blood
2	chr12:124054600-124054800	Enhancers	HepG2	liver
3	chr12:124054600-124056000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr12:124054600-124056200	Enhancers	Fetal Thymus	thymus
5	chr12:124054600-124056400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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