Variant report

Variant	rs17023407
Chromosome Location	chr1:119846698-119846699
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1341799	1.00[AMR][1000 genomes]
rs17023397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17023399	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17023406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17023438	1.00[AMR][1000 genomes]
rs17023448	1.00[AMR][1000 genomes]
rs33920337	1.00[AMR][1000 genomes]
rs4514280	1.00[AMR][1000 genomes]
rs4659155	1.00[AMR][1000 genomes]
rs57010239	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv547615	chr1:119828542-119875730	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	esv2761649	chr1:119840645-119925936	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	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
rs17023407	PGPEP1L	trans	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119844000-119846800	Enhancers	Fetal Brain Male	brain
2	chr1:119845600-119846800	Enhancers	NHDF-Ad	bronchial
3	chr1:119845600-119847400	Enhancers	Fetal Muscle Trunk	muscle
4	chr1:119846000-119846800	Enhancers	Fetal Muscle Leg	muscle
5	chr1:119846000-119847000	Enhancers	Fetal Stomach	stomach
6	chr1:119846200-119846800	Enhancers	Colon Smooth Muscle	Colon
7	chr1:119846200-119846800	Enhancers	HepG2	liver
8	chr1:119846200-119847200	Enhancers	Liver	Liver
9	chr1:119846400-119846800	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr1:119846400-119846800	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:119846400-119847000	Enhancers	Fetal Lung	lung
12	chr1:119846600-119846800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:119846600-119846800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:119846600-119846800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:119846600-119846800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
16	chr1:119846600-119847000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:119846600-119847000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:119846600-119847000	Enhancers	Fetal Intestine Large	intestine

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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