Variant report

Variant	rs12469413
Chromosome Location	chr2:64541127-64541128
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	chr2:64369964..64372694-chr2:64539391..64541388,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197329	Chromatin interaction
ENSG00000225889	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12463946	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12464043	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12475531	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12477412	0.91[CHD][hapmap]
rs12990348	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13013389	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13015766	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13025947	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13029773	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17740892	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1863603	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34631419	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35503140	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36121288	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66495987	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67166439	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67932764	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737470	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7568533	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs872683	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12469413	UGP2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64538200-64543800	Enhancers	Fetal Brain Male	brain
2	chr2:64539800-64543000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:64539800-64549600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:64540000-64554200	Weak transcription	Fetal Brain Female	brain
5	chr2:64540200-64542600	Weak transcription	Esophagus	oesophagus
6	chr2:64540200-64543400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:64540200-64543600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:64540200-64554600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:64540800-64541400	Weak transcription	Fetal Kidney	kidney
10	chr2:64540800-64541800	Weak transcription	Fetal Lung	lung
11	chr2:64540800-64541800	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:64540800-64542000	Weak transcription	Brain Germinal Matrix	brain
13	chr2:64540800-64542200	Weak transcription	Fetal Stomach	stomach
14	chr2:64540800-64542400	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:64540800-64542600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:64540800-64542800	Weak transcription	Fetal Thymus	thymus
17	chr2:64540800-64543400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:64540800-64543600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:64540800-64543600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:64540800-64544200	Weak transcription	Pancreas	Pancrea
21	chr2:64540800-64549600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:64540800-64554600	Weak transcription	Right Atrium	heart
23	chr2:64541000-64542400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:64541000-64542400	Weak transcription	Adipose Nuclei	Adipose

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