Variant report

Variant	rs28454032
Chromosome Location	chr12:124034703-124034704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123873330..123875210-chr12:124033719..124035422,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1057879	0.81[ASN][1000 genomes]
rs10846526	0.95[ASN][1000 genomes]
rs10846528	0.85[ASN][1000 genomes]
rs2048615	0.81[ASN][1000 genomes]
rs2333831	0.81[ASN][1000 genomes]
rs28371124	0.81[ASN][1000 genomes]
rs28403439	0.86[ASN][1000 genomes]
rs28408980	0.82[ASN][1000 genomes]
rs28430750	0.81[ASN][1000 genomes]
rs28465339	0.95[ASN][1000 genomes]
rs28478446	0.81[ASN][1000 genomes]
rs28497190	0.81[ASN][1000 genomes]
rs28498381	0.83[ASN][1000 genomes]
rs28535724	0.86[ASN][1000 genomes]
rs28539789	0.95[ASN][1000 genomes]
rs28654896	0.95[ASN][1000 genomes]
rs28673982	0.86[ASN][1000 genomes]
rs28701527	0.81[ASN][1000 genomes]
rs28707421	0.81[ASN][1000 genomes]
rs28711456	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28712858	0.81[ASN][1000 genomes]
rs28741988	0.81[ASN][1000 genomes]
rs28758342	0.95[ASN][1000 genomes]
rs28834793	0.85[ASN][1000 genomes]
rs4930716	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5027860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61953539	0.86[ASN][1000 genomes]
rs61953543	0.86[ASN][1000 genomes]
rs61953552	0.95[ASN][1000 genomes]
rs61953557	0.95[ASN][1000 genomes]
rs7307227	0.95[ASN][1000 genomes]
rs7313179	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7315326	0.87[ASN][1000 genomes]
rs786454	0.82[ASN][1000 genomes]
rs7959727	0.87[ASN][1000 genomes]
rs7965334	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv976655	chr12:124032880-124035284	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28454032	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs28454032	RP11-486O12.2	cis	Heart Left Ventricle	GTEx
rs28454032	RP11-486O12.2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124034400-124034800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr12:124034400-124039000	Weak transcription	Primary B cells from cord blood	blood
3	chr12:124034600-124034800	Enhancers	Primary hematopoietic stem cells	blood
4	chr12:124034600-124035600	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr12:124034600-124036000	Enhancers	Primary monocytes fromperipheralblood	blood

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