Variant report

Variant	rs442972
Chromosome Location	chr21:40534757-40534758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40534165..40535802-chr21:40542225..40544410,2	MCF-7	breast:
2	chr21:40530945..40533694-chr21:40534297..40536978,4	K562	blood:
3	chr21:40138076..40140463-chr21:40532005..40534792,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235701	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1011413	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10154057	0.81[ASN][1000 genomes]
rs11088471	0.81[AMR][1000 genomes]
rs11088472	0.81[AMR][1000 genomes]
rs11910705	0.80[AMR][1000 genomes]
rs11911112	0.80[AFR][1000 genomes]
rs11911149	0.82[AFR][1000 genomes]
rs11911822	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12626405	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13050247	0.83[ASN][1000 genomes]
rs1571709	0.80[AFR][1000 genomes]
rs1888487	0.85[AMR][1000 genomes]
rs1888488	0.84[AMR][1000 genomes]
rs1980407	0.84[AFR][1000 genomes]
rs2037925	0.83[AMR][1000 genomes]
rs2142111	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2183573	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2245455	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410123	0.83[AMR][1000 genomes]
rs2410124	0.81[AMR][1000 genomes]
rs2836924	0.82[AFR][1000 genomes]
rs2836930	0.81[AFR][1000 genomes]
rs2836969	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836971	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836975	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2836981	0.85[AMR][1000 genomes]
rs2836982	0.85[AMR][1000 genomes]
rs2836986	0.81[AMR][1000 genomes]
rs2836987	0.83[AMR][1000 genomes]
rs2836988	0.83[AMR][1000 genomes]
rs34240248	0.82[AMR][1000 genomes]
rs34436313	0.82[AMR][1000 genomes]
rs35909862	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs371625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs383967	0.83[ASN][1000 genomes]
rs391062	0.83[ASN][1000 genomes]
rs413078	0.83[ASN][1000 genomes]
rs414850	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418359	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419469	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425988	0.83[ASN][1000 genomes]
rs428602	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429955	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444130	0.83[ASN][1000 genomes]
rs452377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452776	0.83[ASN][1000 genomes]
rs4624474	0.82[AMR][1000 genomes]
rs4816620	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4817996	0.82[AFR][1000 genomes]
rs4817999	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818005	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4818015	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4818017	0.85[AMR][1000 genomes]
rs61300849	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6517513	0.82[AFR][1000 genomes]
rs6517514	0.82[AFR][1000 genomes]
rs6517520	0.83[ASN][1000 genomes]
rs6517535	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6650847	0.83[ASN][1000 genomes]
rs66519408	0.83[ASN][1000 genomes]
rs66746936	0.83[ASN][1000 genomes]
rs67212994	0.83[ASN][1000 genomes]
rs67382266	0.81[ASN][1000 genomes]
rs67649754	0.83[ASN][1000 genomes]
rs68086041	0.81[ASN][1000 genomes]
rs68090597	0.85[AFR][1000 genomes]
rs68114370	0.83[ASN][1000 genomes]
rs719230	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7276774	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7278985	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7280326	0.80[AMR][1000 genomes]
rs7281853	0.85[AMR][1000 genomes]
rs7282604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127986	0.85[AMR][1000 genomes]
rs8128191	0.82[AFR][1000 genomes]
rs8130240	0.85[AFR][1000 genomes]
rs8130795	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8130854	0.83[AMR][1000 genomes]
rs8132295	0.82[AFR][1000 genomes]
rs8132333	0.82[AFR][1000 genomes]
rs8132419	0.82[AFR][1000 genomes]
rs8132568	0.81[AFR][1000 genomes]
rs8134214	0.85[AFR][1000 genomes]
rs9636957	0.83[AMR][1000 genomes]
rs997147	0.85[AMR][1000 genomes]
rs9974757	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9978775	0.85[AMR][1000 genomes]
rs9981301	0.80[AMR][1000 genomes]
rs9982111	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9982122	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs442972	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs442972	PSMG1	cis	Esophagus Mucosa	GTEx
rs442972	PSMG1	cis	Nerve Tibial	GTEx
rs442972	PSMG1	cis	Artery Tibial	GTEx
rs442972	PSMG1	cis	lung	GTEx
rs442972	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40532200-40534800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr21:40533600-40545400	Weak transcription	HUVEC	blood vessel

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