Variant report

Variant	rs28589345
Chromosome Location	chr4:120269080-120269081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10000544	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10002914	0.84[ASN][1000 genomes]
rs10006192	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10012408	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10013652	0.84[ASN][1000 genomes]
rs10015579	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10015965	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10016241	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10021601	0.84[ASN][1000 genomes]
rs10022448	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10023641	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10024933	0.80[AFR][1000 genomes]
rs10025925	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10028773	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10029303	0.85[ASN][1000 genomes]
rs10212714	0.80[AFR][1000 genomes]
rs10213158	0.82[AFR][1000 genomes]
rs10434028	0.84[ASN][1000 genomes]
rs10517834	0.84[ASN][1000 genomes]
rs10518300	0.80[AFR][1000 genomes]
rs10857066	0.82[ASN][1000 genomes]
rs11098501	0.80[AFR][1000 genomes]
rs11098502	0.80[AFR][1000 genomes]
rs11098505	0.84[ASN][1000 genomes]
rs11098506	0.84[ASN][1000 genomes]
rs11098507	0.84[ASN][1000 genomes]
rs11724409	0.80[AFR][1000 genomes]
rs11732686	0.80[AFR][1000 genomes]
rs12374244	0.83[ASN][1000 genomes]
rs12374245	0.83[ASN][1000 genomes]
rs12374352	0.83[ASN][1000 genomes]
rs12374396	0.82[ASN][1000 genomes]
rs12498657	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12498994	0.80[AFR][1000 genomes]
rs12499602	0.84[ASN][1000 genomes]
rs12501602	0.83[ASN][1000 genomes]
rs12502393	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12502524	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12503082	0.84[ASN][1000 genomes]
rs12506421	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12506445	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12506487	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12507565	0.80[AFR][1000 genomes]
rs12509621	0.80[AFR][1000 genomes]
rs12510133	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12510451	0.84[ASN][1000 genomes]
rs12510487	0.83[ASN][1000 genomes]
rs12511640	0.80[AFR][1000 genomes]
rs12513083	0.80[AFR][1000 genomes]
rs12513310	0.84[ASN][1000 genomes]
rs13104572	0.85[ASN][1000 genomes]
rs13105020	0.83[ASN][1000 genomes]
rs13125526	0.84[ASN][1000 genomes]
rs13132082	0.84[ASN][1000 genomes]
rs1511017	0.80[AFR][1000 genomes]
rs17009144	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17049949	0.82[AFR][1000 genomes]
rs1814813	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1814814	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1980025	0.80[AFR][1000 genomes]
rs1980026	0.80[AFR][1000 genomes]
rs2002047	0.84[AFR][1000 genomes]
rs2002049	0.84[AFR][1000 genomes]
rs2036860	0.80[AFR][1000 genomes]
rs2136911	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28363929	0.80[AFR][1000 genomes]
rs28369518	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28373117	0.80[AFR][1000 genomes]
rs28396837	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28437684	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28501434	0.84[ASN][1000 genomes]
rs28502463	0.84[AFR][1000 genomes]
rs28546691	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28551750	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28572003	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28581362	0.84[ASN][1000 genomes]
rs28594160	0.86[ASN][1000 genomes]
rs28599836	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28668103	0.84[ASN][1000 genomes]
rs28691602	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28713555	0.80[AFR][1000 genomes]
rs28714087	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28726222	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3864142	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3864144	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4001390	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4107728	0.80[AFR][1000 genomes]
rs4422403	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55820750	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55845118	0.83[ASN][1000 genomes]
rs60378962	0.83[ASN][1000 genomes]
rs67281037	0.85[ASN][1000 genomes]
rs6815291	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6824111	0.84[ASN][1000 genomes]
rs6824169	0.84[ASN][1000 genomes]
rs6838009	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6838457	0.84[AMR][1000 genomes]
rs6846966	0.84[ASN][1000 genomes]
rs6847586	0.84[ASN][1000 genomes]
rs6847778	0.84[ASN][1000 genomes]
rs6847862	0.83[ASN][1000 genomes]
rs6848081	0.86[ASN][1000 genomes]
rs6848380	0.84[ASN][1000 genomes]
rs6857892	0.84[ASN][1000 genomes]
rs72676046	0.80[AFR][1000 genomes]
rs72676059	0.84[ASN][1000 genomes]
rs7677068	0.84[ASN][1000 genomes]
rs7689729	0.82[AFR][1000 genomes]
rs9991221	0.84[ASN][1000 genomes]
rs9991959	0.80[AFR][1000 genomes]
rs9995136	0.84[ASN][1000 genomes]
rs9995716	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28589345	RP11-33B1.1	cis	lung	GTEx
rs28589345	RP11-384K6.6	cis	Whole Blood	GTEx
rs28589345	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs28589345	RP11-33B1.1	cis	Whole Blood	GTEx
rs28589345	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs28589345	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs28589345	RP11-33B1.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120266400-120275000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr4:120269000-120269200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:120269000-120269400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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