Variant report

Variant	rs34125807
Chromosome Location	chr4:120226358-120226359
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11722431	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11722940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724619	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725409	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11725433	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11727970	0.88[ASN][1000 genomes]
rs11727975	0.88[ASN][1000 genomes]
rs11728178	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733606	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11734624	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11734808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737068	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13104050	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13112320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113462	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13113662	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13122306	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13139711	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13140255	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13144426	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1397611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17050312	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17334151	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17517075	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17517470	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595769	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595790	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036859	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34156358	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34733524	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878806	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34951506	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35137697	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35225855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612705	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35646004	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35846514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35917388	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817230	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817242	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56818816	0.95[ASN][1000 genomes]
rs62320715	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320716	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320717	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320718	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320719	0.91[ASN][1000 genomes]
rs62320720	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320721	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320722	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320723	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320724	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320725	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320731	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320732	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320733	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320735	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320737	1.00[ASN][1000 genomes]
rs62322274	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62322275	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62322276	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62328380	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328402	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328403	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328404	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328420	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822097	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71627784	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72918504	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34125807	USP53	cis	Whole Blood	GTEx
rs34125807	RP11-33B1.1	cis	Thyroid	GTEx
rs34125807	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120222000-120251000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:120222200-120244600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:120222400-120227800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:120222400-120229000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:120222400-120240800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:120222800-120240800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:120223200-120227800	Weak transcription	Fetal Intestine Large	intestine
8	chr4:120225000-120238800	Weak transcription	Fetal Intestine Small	intestine

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