Variant report

Variant	rs56209573
Chromosome Location	chr5:112294156-112294157
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112256942..112259777-chr5:112292490..112295980,4	MCF-7	breast:
2	chr5:112256312..112258572-chr5:112293343..112296094,6	MCF-7	breast:
3	chr5:112252458..112254818-chr5:112292295..112294312,2	K562	blood:
4	chr5:112293295..112296045-chr5:112298149..112301329,3	MCF-7	breast:
5	chr5:112292808..112297954-chr5:112311731..112314309,4	MCF-7	breast:
6	chr5:112292660..112295480-chr5:112309614..112313888,4	K562	blood:

Variant related genes	Relation type
ENSG00000129625	Chromatin interaction
ENSG00000172795	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10447234	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10515450	1.00[ASN][1000 genomes]
rs10515451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515452	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11241186	0.80[EUR][1000 genomes]
rs12152818	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12152991	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12187307	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188113	1.00[ASN][1000 genomes]
rs17135215	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17553240	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55915006	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56315627	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56364425	1.00[ASN][1000 genomes]
rs56398453	0.83[ASN][1000 genomes]
rs58304718	0.92[EUR][1000 genomes]
rs73789249	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73789251	1.00[ASN][1000 genomes]
rs73789252	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73789253	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73789254	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];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	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56209573	DCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112291600-112297600	Enhancers	HepG2	liver
2	chr5:112291800-112294400	Enhancers	Brain Germinal Matrix	brain
3	chr5:112292200-112294400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:112292600-112294200	Flanking Active TSS	A549	lung
5	chr5:112292600-112295000	Enhancers	Hela-S3	cervix
6	chr5:112292600-112295200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr5:112292800-112294800	Enhancers	Fetal Brain Female	brain
8	chr5:112292800-112295200	Enhancers	Adipose Nuclei	Adipose
9	chr5:112292800-112295600	Weak transcription	Lung	lung
10	chr5:112293000-112294400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:112293000-112295200	Enhancers	Liver	Liver
12	chr5:112293200-112294200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:112293200-112294200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:112293200-112294400	Enhancers	Fetal Brain Male	brain
15	chr5:112293200-112294600	Enhancers	Osteobl	bone
16	chr5:112293200-112294800	Enhancers	Brain Angular Gyrus	brain
17	chr5:112293200-112295000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr5:112293200-112295200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr5:112293200-112296400	Enhancers	Stomach Smooth Muscle	stomach
20	chr5:112293200-112296400	Enhancers	HSMMtube	muscle
21	chr5:112293200-112296400	Enhancers	HUVEC	blood vessel
22	chr5:112293200-112297000	Enhancers	NHDF-Ad	bronchial
23	chr5:112293200-112297000	Enhancers	NHLF	lung
24	chr5:112293400-112297200	Enhancers	Fetal Muscle Leg	muscle
25	chr5:112293400-112297200	Enhancers	Fetal Stomach	stomach
26	chr5:112293600-112295200	Enhancers	Fetal Lung	lung
27	chr5:112293600-112296400	Enhancers	HSMM	muscle
28	chr5:112293800-112294200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:112293800-112294200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr5:112293800-112294200	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr5:112293800-112294200	Enhancers	Psoas Muscle	Psoas
32	chr5:112293800-112294400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:112293800-112294400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:112293800-112294400	Enhancers	Aorta	Aorta
35	chr5:112293800-112294400	Enhancers	Pancreas	Pancrea
36	chr5:112293800-112294400	Enhancers	Rectal Smooth Muscle	rectum
37	chr5:112293800-112294400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr5:112293800-112294600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr5:112293800-112294600	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr5:112293800-112294600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr5:112293800-112294800	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr5:112293800-112294800	Enhancers	Fetal Heart	heart
43	chr5:112293800-112294800	Enhancers	Small Intestine	intestine
44	chr5:112293800-112295000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:112293800-112295000	Enhancers	Brain Hippocampus Middle	brain
46	chr5:112293800-112295200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:112293800-112295800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:112293800-112296000	Enhancers	Colon Smooth Muscle	Colon
49	chr5:112293800-112296000	Enhancers	Stomach Mucosa	stomach
50	chr5:112293800-112296000	Enhancers	HMEC	breast

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