Variant report

Variant	rs13047550
Chromosome Location	chr21:40515495-40515496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40500620..40503419-chr21:40514957..40517352,2	MCF-7	breast:
2	chr21:40187682..40190648-chr21:40515051..40517560,2	K562	blood:
3	chr21:40515045..40517446-chr21:40522211..40524876,3	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1065242	0.91[EUR][1000 genomes]
rs11910151	0.91[EUR][1000 genomes]
rs11911112	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11911149	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12481860	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12482156	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482181	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12482857	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12483216	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12710453	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13048178	0.92[EUR][1000 genomes]
rs13049280	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13052882	0.93[EUR][1000 genomes]
rs13339986	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs14194	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1571709	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1984022	0.84[EUR][1000 genomes]
rs2026265	0.84[EUR][1000 genomes]
rs2234543	0.90[EUR][1000 genomes]
rs2836920	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2836921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836923	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836924	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836925	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836927	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836928	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836929	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836932	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836933	0.92[EUR][1000 genomes]
rs2836938	0.90[EUR][1000 genomes]
rs2836944	0.83[EUR][1000 genomes]
rs34035316	0.84[EUR][1000 genomes]
rs34176878	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34294410	0.93[EUR][1000 genomes]
rs34394827	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34478864	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34592564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34978594	0.84[EUR][1000 genomes]
rs35064900	0.92[EUR][1000 genomes]
rs35386515	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35391055	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35571600	0.83[EUR][1000 genomes]
rs35774464	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36113648	0.93[EUR][1000 genomes]
rs3945	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4817996	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56049536	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56112725	0.86[EUR][1000 genomes]
rs56306759	0.81[EUR][1000 genomes]
rs6517513	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517514	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517519	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517521	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517523	0.92[EUR][1000 genomes]
rs6517526	0.85[EUR][1000 genomes]
rs6517527	0.84[EUR][1000 genomes]
rs66465538	0.80[AMR][1000 genomes]
rs68090597	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71184665	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7280375	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73221174	0.87[EUR][1000 genomes]
rs73221193	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8127087	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8128026	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8128102	0.82[EUR][1000 genomes]
rs8128191	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8128734	0.91[EUR][1000 genomes]
rs8129355	0.84[EUR][1000 genomes]
rs8130556	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8131965	0.85[EUR][1000 genomes]
rs8132295	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132333	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132419	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132568	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][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	esv3395554	chr21:40512728-40517052	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13047550	PSMG1	cis	Esophagus Mucosa	GTEx
rs13047550	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40509800-40515800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr21:40514200-40517000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:40514200-40520200	Weak transcription	Psoas Muscle	Psoas
4	chr21:40515000-40515600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr21:40515000-40516400	Enhancers	Fetal Muscle Leg	muscle

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