Variant report

Variant	rs13020490
Chromosome Location	chr2:55135551-55135552
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	chr2:55135110..55137315-chr2:55274820..55277436,2	MCF-7	breast:
2	chr2:55131952..55133594-chr2:55135173..55137176,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10196667	1.00[ASN][1000 genomes]
rs10746530	1.00[ASN][1000 genomes]
rs11125551	0.94[ASN][1000 genomes]
rs11904457	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12475185	0.97[ASN][1000 genomes]
rs13008105	0.97[ASN][1000 genomes]
rs13026576	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13028800	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17418111	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2304685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36024305	0.97[ASN][1000 genomes]
rs36063689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4233956	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4504034	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4525735	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4671233	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4671998	1.00[ASN][1000 genomes]
rs55777421	1.00[ASN][1000 genomes]
rs61910689	0.90[AFR][1000 genomes]
rs6545462	0.97[ASN][1000 genomes]
rs67721747	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13020490	RTN4	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55095200-55148200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55132000-55136600	Enhancers	Liver	Liver
3	chr2:55132000-55140600	Weak transcription	Esophagus	oesophagus
4	chr2:55132200-55135600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:55132200-55135800	Weak transcription	NH-A	brain
6	chr2:55132400-55135600	Weak transcription	Osteobl	bone
7	chr2:55132400-55135800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:55132400-55135800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:55132600-55135600	Weak transcription	HepG2	liver
10	chr2:55133000-55135600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:55133200-55135600	Weak transcription	NHLF	lung
12	chr2:55133600-55135600	Weak transcription	Fetal Intestine Small	intestine
13	chr2:55134000-55135600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:55134000-55153800	Weak transcription	Brain Angular Gyrus	brain
15	chr2:55134200-55135600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:55134200-55135600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:55134200-55135600	Weak transcription	Psoas Muscle	Psoas
18	chr2:55134200-55135600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:55134200-55135600	Weak transcription	HSMM	muscle
20	chr2:55134200-55135600	Weak transcription	HSMMtube	muscle
21	chr2:55134200-55147600	Weak transcription	Fetal Brain Female	brain
22	chr2:55134400-55135800	Weak transcription	Fetal Heart	heart
23	chr2:55134400-55153600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:55134600-55135800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:55135200-55137800	Enhancers	NHDF-Ad	bronchial
26	chr2:55135400-55135600	Enhancers	Fetal Muscle Trunk	muscle
27	chr2:55135400-55136200	Enhancers	Fetal Muscle Leg	muscle

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