Variant report

Variant	rs12873457
Chromosome Location	chr13:52479690-52479691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52478432..52480213-chr13:52499917..52502215,2	MCF-7	breast:
2	chr13:52473231..52476356-chr13:52478629..52481911,3	K562	blood:
3	chr13:52473231..52476080-chr13:52478629..52481911,3	K562	blood:
4	chr13:52474695..52476604-chr13:52478889..52481158,2	MCF-7	breast:
5	chr13:52478878..52481837-chr13:52486558..52489316,5	MCF-7	breast:
6	chr13:52421639..52423143-chr13:52479178..52481096,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12873127	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34038648	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34310786	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34752340	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35102401	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35181830	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35702891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8002491	1.00[CHD][hapmap]
rs9535789	0.83[EUR][1000 genomes]
rs9596610	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12873457	ATP7B	cis	cerebellum	SCAN
rs12873457	NCRNA00282	cis	cerebellum	SCAN
rs12873457	MED4	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52457400-52480200	Weak transcription	Liver	Liver
2	chr13:52464600-52494400	Weak transcription	Aorta	Aorta
3	chr13:52467600-52480400	Weak transcription	Fetal Lung	lung
4	chr13:52470800-52481000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr13:52475600-52493800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:52476200-52480400	Weak transcription	Pancreas	Pancrea
7	chr13:52476200-52493800	Weak transcription	K562	blood
8	chr13:52476400-52496600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr13:52477000-52481800	Strong transcription	Fetal Intestine Small	intestine
10	chr13:52477600-52480800	Weak transcription	Right Ventricle	heart
11	chr13:52477600-52481800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr13:52478600-52480200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:52479000-52481000	Weak transcription	Gastric	stomach
14	chr13:52479000-52481400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr13:52479200-52479800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr13:52479200-52479800	Enhancers	Spleen	Spleen
17	chr13:52479200-52480000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr13:52479200-52480200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr13:52479400-52479800	Enhancers	Fetal Thymus	thymus
20	chr13:52479400-52480200	Enhancers	H9 Cell Line	embryonic stem cell
21	chr13:52479400-52480200	Strong transcription	HepG2	liver
22	chr13:52479400-52480600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr13:52479400-52480800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr13:52479400-52481600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:52479400-52491000	Weak transcription	Fetal Intestine Large	intestine
26	chr13:52479600-52479800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr13:52479600-52479800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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