Variant report

Variant	rs17296412
Chromosome Location	chr4:120656753-120656754
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10016938	1.00[ASN][1000 genomes]
rs11722660	1.00[ASN][1000 genomes]
rs11723555	0.82[EUR][1000 genomes]
rs11726524	1.00[ASN][1000 genomes]
rs11730012	1.00[ASN][1000 genomes]
rs11731926	1.00[ASN][1000 genomes]
rs11732719	1.00[ASN][1000 genomes]
rs13119468	0.82[EUR][1000 genomes]
rs17005450	1.00[ASN][1000 genomes]
rs17005667	1.00[ASN][1000 genomes]
rs17295253	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17296659	0.82[EUR][1000 genomes]
rs2389960	0.82[EUR][1000 genomes]
rs2583599	0.81[EUR][1000 genomes]
rs28587671	0.82[EUR][1000 genomes]
rs35428685	1.00[ASN][1000 genomes]
rs3857096	1.00[ASN][1000 genomes]
rs55685100	1.00[ASN][1000 genomes]
rs55717715	1.00[ASN][1000 genomes]
rs55788903	0.91[ASN][1000 genomes]
rs55929181	1.00[ASN][1000 genomes]
rs56291824	1.00[ASN][1000 genomes]
rs56336246	0.91[ASN][1000 genomes]
rs56337310	1.00[ASN][1000 genomes]
rs57160305	1.00[ASN][1000 genomes]
rs58342688	1.00[ASN][1000 genomes]
rs59063054	1.00[ASN][1000 genomes]
rs60849110	1.00[ASN][1000 genomes]
rs61595361	0.82[ASN][1000 genomes]
rs61707138	1.00[ASN][1000 genomes]
rs722808	0.91[ASN][1000 genomes]
rs72906506	1.00[ASN][1000 genomes]
rs72906508	1.00[ASN][1000 genomes]
rs72906511	1.00[ASN][1000 genomes]
rs72906573	0.91[ASN][1000 genomes]
rs73842698	1.00[ASN][1000 genomes]
rs73842716	1.00[ASN][1000 genomes]
rs9968281	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1802546	chr4:120558608-120675026	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1010638	chr4:120586178-120671835	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1009771	chr4:120590902-120665812	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv1803992	chr4:120649398-120665812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17296412	USP53	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120649600-120658200	Enhancers	NHLF	lung
2	chr4:120650200-120658000	Enhancers	HSMMtube	muscle
3	chr4:120650200-120658400	Enhancers	NHDF-Ad	bronchial
4	chr4:120650400-120657200	Weak transcription	Psoas Muscle	Psoas
5	chr4:120651600-120658000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:120652000-120658600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:120652200-120658200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr4:120653200-120657200	Weak transcription	Aorta	Aorta
9	chr4:120654400-120658800	Enhancers	Osteobl	bone
10	chr4:120654600-120658200	Enhancers	NH-A	brain
11	chr4:120654800-120658000	Enhancers	HSMM	muscle
12	chr4:120654800-120658800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:120655400-120657400	Enhancers	Fetal Lung	lung
14	chr4:120655600-120657200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:120655800-120657000	Enhancers	HMEC	breast
16	chr4:120655800-120657400	Enhancers	Colon Smooth Muscle	Colon
17	chr4:120655800-120658000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:120656000-120656800	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr4:120656000-120656800	Enhancers	Fetal Stomach	stomach
20	chr4:120656000-120656800	Enhancers	Stomach Mucosa	stomach
21	chr4:120656000-120657000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:120656000-120657000	Enhancers	Fetal Heart	heart
23	chr4:120656000-120657200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:120656000-120658000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr4:120656000-120658200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:120656200-120656800	Enhancers	Fetal Kidney	kidney
27	chr4:120656200-120656800	Enhancers	A549	lung
28	chr4:120656200-120657200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr4:120656200-120658400	Enhancers	Rectal Smooth Muscle	rectum
30	chr4:120656400-120656800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr4:120656600-120659800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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