Variant report

Variant	rs13106925
Chromosome Location	chr4:120539108-120539109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10022664	0.85[JPT][hapmap]
rs10025536	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724055	0.83[EUR][1000 genomes]
rs11730798	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11731568	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103510	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13103899	0.82[EUR][1000 genomes]
rs13109926	0.84[EUR][1000 genomes]
rs13116789	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs13118388	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120581	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13121569	0.82[EUR][1000 genomes]
rs13124532	0.85[EUR][1000 genomes]
rs13133969	0.85[EUR][1000 genomes]
rs13136296	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137511	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13140150	0.85[EUR][1000 genomes]
rs13147817	0.94[EUR][1000 genomes]
rs17292047	1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17358524	1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17358860	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2389868	1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2389870	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2892870	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2953295	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34601943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34676199	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35289699	0.84[EUR][1000 genomes]
rs35581370	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35850447	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35967840	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35999787	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733526	0.85[JPT][hapmap]
rs3756155	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756157	0.85[JPT][hapmap]
rs3775846	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3775850	0.84[EUR][1000 genomes]
rs3775851	0.84[EUR][1000 genomes]
rs3775856	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4597811	0.85[JPT][hapmap]
rs4833620	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4834782	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4834788	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834789	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834790	1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61747388	0.82[EUR][1000 genomes]
rs62319606	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62319609	0.85[EUR][1000 genomes]
rs62319612	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62319647	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62319657	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62319658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62321168	0.85[EUR][1000 genomes]
rs6534146	0.85[JPT][hapmap]
rs6817975	1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847164	0.85[JPT][hapmap]
rs7672961	0.85[JPT][hapmap]
rs7676589	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13106925	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs13106925	USP53	cis	Whole Blood	GTEx
rs13106925	RP11-33B1.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
3	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:120521000-120544800	Weak transcription	Fetal Intestine Large	intestine
5	chr4:120526200-120546800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:120526400-120544200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:120528400-120547400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:120528600-120547400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:120528600-120547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:120528800-120540200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:120528800-120543000	Weak transcription	Pancreas	Pancrea
12	chr4:120528800-120544200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:120528800-120545400	Weak transcription	Fetal Stomach	stomach
14	chr4:120529000-120546600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:120532400-120547600	Weak transcription	Lung	lung
16	chr4:120533000-120544200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:120533600-120539200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:120533600-120547400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:120534000-120547400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:120537000-120547400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:120537200-120542400	Enhancers	Fetal Lung	lung
22	chr4:120537800-120541000	Weak transcription	Aorta	Aorta
23	chr4:120538200-120539800	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:120538400-120539400	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr4:120538600-120539200	Weak transcription	Osteobl	bone
26	chr4:120538600-120540000	Weak transcription	NHLF	lung
27	chr4:120538600-120540800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:120538600-120542000	Weak transcription	Small Intestine	intestine
29	chr4:120538800-120539200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr4:120538800-120539600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:120539000-120540600	Enhancers	Stomach Smooth Muscle	stomach
32	chr4:120539000-120541000	Enhancers	Rectal Smooth Muscle	rectum

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