Variant report

Variant	rs71627784
Chromosome Location	chr4:120244902-120244903
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11722431	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11722940	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724619	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11725409	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11725433	0.96[EUR][1000 genomes]
rs11728178	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11729960	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11733606	0.93[EUR][1000 genomes]
rs11734624	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11734808	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11736997	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11737068	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13104050	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13112320	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13113462	0.95[EUR][1000 genomes]
rs13113662	0.93[EUR][1000 genomes]
rs13122306	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13127517	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13139711	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13140255	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13144426	0.97[EUR][1000 genomes]
rs1397611	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17050312	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17334151	0.89[EUR][1000 genomes]
rs17517075	0.99[EUR][1000 genomes]
rs17517470	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17595468	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17595769	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17595790	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2036859	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34125807	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34156358	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34733524	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34878806	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34951506	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35137697	0.91[EUR][1000 genomes]
rs35225855	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35612705	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35646004	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35846514	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35917388	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817230	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817242	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56818816	0.85[ASN][1000 genomes]
rs62320715	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320716	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320717	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320718	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320719	0.90[ASN][1000 genomes]
rs62320720	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320721	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320722	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320723	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320724	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320725	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320731	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320732	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320733	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320735	0.91[ASN][1000 genomes]
rs62320737	0.91[ASN][1000 genomes]
rs62322274	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62322275	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62322276	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62328380	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62328402	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62328403	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62328404	0.97[EUR][1000 genomes]
rs62328408	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62328420	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6822097	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72918504	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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
5	nsv879840	chr4:120227419-120257417	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv2525765	chr4:120243529-120245168	Weak transcription Flanking Active TSS Active TSS Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	esv3346833	chr4:120243754-120245852	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
8	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv2018154	chr4:120244361-120245100	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
11	esv8767	chr4:120244404-120245164	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
12	esv3466094	chr4:120244454-120245001	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
13	esv3517491	chr4:120244459-120245048	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
14	esv3517489	chr4:120244463-120245007	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
15	esv3517487	chr4:120244484-120244968	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
16	esv3466092	chr4:120244496-120244976	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
17	esv3466091	chr4:120244498-120245049	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
18	esv3517490	chr4:120244507-120244968	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
19	esv3432674	chr4:120244508-120244961	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
20	esv3466095	chr4:120244512-120244933	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
21	esv3466093	chr4:120244543-120244911	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
22	esv3517488	chr4:120244558-120244904	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
23	nsv290888	chr4:120244559-120244903	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
24	esv3466096	chr4:120244559-120244919	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
25	esv3517492	chr4:120244559-120244919	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
26	nsv290094	chr4:120244574-120244918	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs71627784	RP11-33B1.1	cis	Thyroid	GTEx
rs71627784	USP53	cis	Whole Blood	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120222000-120251000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:120235600-120251000	Weak transcription	Left Ventricle	heart
3	chr4:120243600-120245200	Enhancers	Fetal Intestine Large	intestine
4	chr4:120244000-120245400	Enhancers	Fetal Intestine Small	intestine
5	chr4:120244400-120249800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:120244800-120245200	Enhancers	Rectal Mucosa Donor 31	rectum

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