Variant report

Variant	rs825457
Chromosome Location	chr12:124538302-124538303
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124538115..124539228-chr12:124805608..124806447,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10846598	1.00[ASN][1000 genomes]
rs1631624	1.00[ASN][1000 genomes]
rs1686728	1.00[ASN][1000 genomes]
rs1716378	1.00[ASN][1000 genomes]
rs1716385	1.00[ASN][1000 genomes]
rs1716403	1.00[ASN][1000 genomes]
rs1716409	1.00[ASN][1000 genomes]
rs2451323	1.00[ASN][1000 genomes]
rs2451325	1.00[ASN][1000 genomes]
rs4765041	1.00[ASN][1000 genomes]
rs707333	1.00[ASN][1000 genomes]
rs7138055	1.00[ASN][1000 genomes]
rs825454	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs825464	1.00[ASN][1000 genomes]
rs825466	1.00[ASN][1000 genomes]
rs825479	1.00[ASN][1000 genomes]
rs825497	1.00[ASN][1000 genomes]
rs861131	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs866640	1.00[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	nsv899580	chr12:124499542-124565258	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv455734	chr12:124511908-124772515	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv560538	chr12:124511908-124772515	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs825457	CCDC92	cis	cerebellum	SCAN
rs825457	CCDC92	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124530600-124539000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:124534600-124538400	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:124534600-124538400	Weak transcription	Stomach Mucosa	stomach
4	chr12:124534800-124538600	Weak transcription	Fetal Heart	heart
5	chr12:124537200-124538400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:124537600-124539000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:124537600-124539200	Enhancers	Fetal Stomach	stomach
8	chr12:124537600-124539400	Enhancers	Placenta	Placenta
9	chr12:124538000-124538800	Enhancers	Fetal Thymus	thymus
10	chr12:124538200-124538400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:124538200-124538400	Enhancers	Fetal Kidney	kidney
12	chr12:124538200-124538600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:124538200-124538600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:124538200-124538600	Flanking Active TSS	HUVEC	blood vessel
15	chr12:124538200-124538800	Enhancers	HepG2	liver
16	chr12:124538200-124539000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:124538200-124539000	Enhancers	Brain Hippocampus Middle	brain
18	chr12:124538200-124539200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:124538200-124539200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr12:124538200-124539200	Enhancers	Brain Substantia Nigra	brain
21	chr12:124538200-124539200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr12:124538200-124539200	Enhancers	Fetal Brain Male	brain
23	chr12:124538200-124539200	Enhancers	Fetal Lung	lung

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