Variant report

Variant	rs62320725
Chromosome Location	chr4:120275268-120275269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11722431	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11722940	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724619	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725409	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11725433	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11727068	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11727963	0.99[AFR][1000 genomes]
rs11727970	0.88[ASN][1000 genomes]
rs11727975	0.88[ASN][1000 genomes]
rs11728178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729960	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733606	0.81[ASN][1000 genomes]
rs11734624	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11734808	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735260	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11736997	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737068	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13101369	0.80[EUR][1000 genomes]
rs13104050	0.81[ASN][1000 genomes]
rs13112320	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113462	0.81[ASN][1000 genomes]
rs13113662	0.81[ASN][1000 genomes]
rs13122306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127517	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13139711	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13140255	0.81[ASN][1000 genomes]
rs13144426	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1397611	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17050312	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17334151	0.81[ASN][1000 genomes]
rs17517075	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17517470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595468	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036859	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34125807	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34156358	0.81[ASN][1000 genomes]
rs34733524	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878806	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34951506	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35137697	0.81[ASN][1000 genomes]
rs35225855	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612705	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35646004	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35846514	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35917388	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56818816	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57153990	0.86[AFR][1000 genomes]
rs58536775	0.80[EUR][1000 genomes]
rs60058568	0.86[AFR][1000 genomes]
rs62320715	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320716	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320717	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320719	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62320720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320721	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320733	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320735	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320737	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62320741	0.92[EUR][1000 genomes]
rs62322274	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62322275	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62322276	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62328380	0.81[ASN][1000 genomes]
rs62328402	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328403	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328404	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328408	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328420	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822097	0.91[ASN][1000 genomes]
rs71627784	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72918504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv964091	chr4:120255342-120290951	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases
10	esv3512786	chr4:120275104-120279402	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
11	esv3512787	chr4:120275104-120279402	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62320725	RP11-33B1.1	cis	Muscle Skeletal	GTEx
rs62320725	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs62320725	RP11-33B1.1	cis	Thyroid	GTEx
rs62320725	RP11-33B1.1	cis	Nerve Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120269200-120277600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr4:120269600-120293000	Weak transcription	Fetal Heart	heart
3	chr4:120274400-120275400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:120274400-120275400	Enhancers	NHEK	skin
5	chr4:120274800-120275400	Enhancers	HMEC	breast

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