Variant report

Variant	rs6517514
Chromosome Location	chr21:40527095-40527096
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40524814..40527539-chr21:40530496..40533251,3	K562	blood:
2	chr21:40526392..40529337-chr21:40554879..40556594,2	MCF-7	breast:
3	21:40526994-40534295..21:40748850-40752541	K562	blood:

Variant related genes	Relation type
ENSG00000183527	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1065242	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11910151	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11911112	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11911149	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481860	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482156	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12482181	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482857	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12483216	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12710453	0.84[EUR][1000 genomes]
rs13047550	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13048178	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13049280	0.85[EUR][1000 genomes]
rs13052882	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13339986	0.84[EUR][1000 genomes]
rs14194	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541102	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1571709	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984022	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2026265	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2150415	0.81[EUR][1000 genomes]
rs2234543	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836920	0.80[ASN][1000 genomes]
rs2836921	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836923	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836924	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836925	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836927	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836928	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836929	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836932	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836933	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2836938	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836944	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836964	0.82[AMR][1000 genomes]
rs34035316	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34176878	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34294410	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34394827	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34478864	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34592564	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34978594	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35064900	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35386515	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35391055	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571600	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35774464	0.85[EUR][1000 genomes]
rs36113648	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs371625	0.82[AFR][1000 genomes]
rs377098	0.82[AFR][1000 genomes]
rs3945	0.94[EUR][1000 genomes]
rs414850	0.82[AFR][1000 genomes]
rs418298	0.82[AFR][1000 genomes]
rs418359	0.81[AFR][1000 genomes]
rs419469	0.82[AFR][1000 genomes]
rs429955	0.82[AFR][1000 genomes]
rs442972	0.82[AFR][1000 genomes]
rs452377	0.82[AFR][1000 genomes]
rs4817996	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56049536	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56112725	0.87[EUR][1000 genomes]
rs56306759	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6517513	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517519	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517521	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517523	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6517526	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6517527	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs68090597	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71184665	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280375	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282604	0.82[AFR][1000 genomes]
rs73221174	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73221193	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127087	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128026	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128102	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8128191	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128734	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8129355	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8130556	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8131965	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8132295	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132333	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132419	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132568	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8133146	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2153623	chr21:40527095-40527096	Weak transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6517514	PSMG1	cis	Esophagus Mucosa	GTEx
rs6517514	PSMG1	cis	Nerve Tibial	GTEx
rs6517514	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs6517514	PSMG1	cis	Artery Tibial	GTEx
rs6517514	PSMG1	cis	Muscle Skeletal	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40526000-40531000	Weak transcription	Fetal Muscle Leg	muscle
2	chr21:40526000-40531000	Weak transcription	HSMMtube	muscle

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