Variant report

Variant	rs17254013
Chromosome Location	chr8:124591972-124591973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:124575271..124580118-chr8:124587417..124591995,7	MCF-7	breast:
2	chr8:124576148..124579059-chr8:124591482..124593021,2	MCF-7	breast:
3	chr8:124589966..124594613-chr8:124606326..124610133,5	MCF-7	breast:
4	chr8:124591963..124593742-chr8:124625579..124627436,2	MCF-7	breast:
5	chr8:124591472..124593907-chr8:124596529..124599826,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253286	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10216826	1.00[CHB][hapmap]
rs10956124	1.00[CHB][hapmap]
rs10956138	1.00[CHB][hapmap]
rs12547295	1.00[CHB][hapmap]
rs4529453	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4871375	1.00[CHB][hapmap]
rs4871387	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs4871388	0.81[CEU][hapmap]
rs4871389	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62518431	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62518436	0.90[EUR][1000 genomes]
rs62520861	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62520864	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62520865	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62520872	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62520912	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6470148	1.00[CHB][hapmap]
rs7005105	1.00[CHB][hapmap]
rs9297669	1.00[CHB][hapmap]

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	nsv831450	chr8:124471741-124661359	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17254013	TRMT12	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:124575600-124598600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:124587400-124592000	Weak transcription	HSMM	muscle
3	chr8:124587400-124592200	Weak transcription	Placenta	Placenta
4	chr8:124588400-124592800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr8:124588800-124592200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr8:124589600-124593600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr8:124590000-124592400	Weak transcription	Fetal Intestine Large	intestine
8	chr8:124590800-124592000	Weak transcription	HMEC	breast
9	chr8:124590800-124593000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr8:124590800-124597000	Weak transcription	HSMMtube	muscle
11	chr8:124591000-124594600	Enhancers	Fetal Intestine Small	intestine
12	chr8:124591600-124592000	Enhancers	Brain Hippocampus Middle	brain
13	chr8:124591600-124592000	Enhancers	Psoas Muscle	Psoas
14	chr8:124591600-124592400	Enhancers	Pancreas	Pancrea
15	chr8:124591600-124593000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr8:124591600-124593000	Enhancers	NHDF-Ad	bronchial
17	chr8:124591600-124593800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr8:124591600-124594000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:124591600-124594000	Enhancers	Fetal Heart	heart
20	chr8:124591600-124594200	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr8:124591600-124594400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr8:124591800-124592000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr8:124591800-124592200	Enhancers	A549	lung
24	chr8:124591800-124592800	Enhancers	Hela-S3	cervix
25	chr8:124591800-124593400	Weak transcription	Fetal Muscle Leg	muscle
26	chr8:124591800-124593800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr8:124591800-124594200	Enhancers	Osteobl	bone

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