Variant report

Variant	rs17074015
Chromosome Location	chr13:30485826-30485827
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	chr13:30482306..30489173-chr13:30491895..30500288,16	MCF-7	breast:
2	chr13:30422892..30425150-chr13:30482194..30486036,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122042	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11616970	1.00[ASN][1000 genomes]
rs11617644	0.99[ASN][1000 genomes]
rs11618111	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11843877	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17074040	0.85[JPT][hapmap]
rs17631508	0.89[ASN][1000 genomes]
rs2027459	1.00[ASN][1000 genomes]
rs2027460	1.00[ASN][1000 genomes]
rs2031491	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2031492	1.00[ASN][1000 genomes]
rs2039948	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2039951	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34444526	1.00[ASN][1000 genomes]
rs56144866	1.00[ASN][1000 genomes]
rs60031463	0.97[ASN][1000 genomes]
rs61947281	1.00[ASN][1000 genomes]
rs7994117	1.00[ASN][1000 genomes]
rs912790	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs912791	1.00[ASN][1000 genomes]
rs912792	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs927735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9314988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9508589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17074015	USP12	cis	cerebellum	SCAN
rs17074015	EEF1DP3	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30476800-30497600	Weak transcription	Right Atrium	heart
2	chr13:30477000-30492400	Weak transcription	Pancreas	Pancrea
3	chr13:30477400-30486000	Weak transcription	Adipose Nuclei	Adipose
4	chr13:30481400-30494000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr13:30482800-30486000	Weak transcription	Gastric	stomach
6	chr13:30483600-30489200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr13:30484800-30486000	Weak transcription	Esophagus	oesophagus
8	chr13:30484800-30486000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr13:30484800-30486000	Weak transcription	Fetal Muscle Leg	muscle
10	chr13:30484800-30486000	Weak transcription	Placenta	Placenta
11	chr13:30484800-30486200	Weak transcription	HSMM	muscle
12	chr13:30484800-30491200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr13:30484800-30491200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:30484800-30492400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:30485000-30486000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr13:30485000-30486000	Weak transcription	NHDF-Ad	bronchial
17	chr13:30485000-30494200	Weak transcription	A549	lung
18	chr13:30485200-30486400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr13:30485400-30486000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:30485600-30486200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:30485800-30486400	Enhancers	Stomach Mucosa	stomach

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