Variant report

Variant	rs4834782
Chromosome Location	chr4:120497139-120497140
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10025536	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11724055	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11730798	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11731568	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13103510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103899	0.83[EUR][1000 genomes]
rs13106925	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13109926	0.82[EUR][1000 genomes]
rs13116789	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13118388	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13120581	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13121569	0.83[EUR][1000 genomes]
rs13124532	0.86[EUR][1000 genomes]
rs13133969	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13136296	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13137511	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140150	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13147817	0.92[EUR][1000 genomes]
rs17292047	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17358524	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17358860	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2389868	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389870	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2892870	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2953295	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34601943	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34676199	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35289699	0.85[EUR][1000 genomes]
rs35581370	0.89[EUR][1000 genomes]
rs35850447	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35967840	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35999787	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756155	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3775846	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3775850	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3775851	0.85[EUR][1000 genomes]
rs3775856	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4833620	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4834788	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4834789	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4834790	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61747388	0.83[EUR][1000 genomes]
rs62319606	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62319609	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62319612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62319647	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62319657	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62319658	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62321168	0.83[EUR][1000 genomes]
rs6817975	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7676589	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
rs4834782	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs4834782	RP11-33B1.1	cis	Thyroid	GTEx
rs4834782	USP53	cis	Whole Blood	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
2	chr4:120478600-120501000	Weak transcription	Fetal Stomach	stomach
3	chr4:120485800-120503800	Weak transcription	Aorta	Aorta
4	chr4:120485800-120520000	Weak transcription	Small Intestine	intestine
5	chr4:120486200-120503800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:120486200-120504800	Weak transcription	NH-A	brain
7	chr4:120486600-120502800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:120486600-120516600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:120486800-120503600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:120486800-120515800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:120486800-120516400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:120488000-120501000	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:120488200-120501200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:120488200-120510200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:120488400-120504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:120492200-120502000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:120492200-120513800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:120492400-120501200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:120492400-120501600	Weak transcription	Fetal Lung	lung
22	chr4:120493400-120498400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:120493400-120501000	Weak transcription	Osteobl	bone
24	chr4:120494200-120501000	Weak transcription	NHLF	lung
25	chr4:120495600-120501000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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