Variant report

Variant	rs6064043
Chromosome Location	chr20:52690458-52690459
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr20:52690431-52694002	MCF-7	breast:	n/a	chr20:52691423-52691431

No.	Distal block	Cell Line	Cell type
1	chr17:56734557..56739323-chr20:52682038..52691817,18	MCF-7	breast:
2	chr17:56707573..56710452-chr20:52690315..52697249,11	MCF-7	breast:
3	chr1:92763250..92765848-chr20:52689571..52691087,2	MCF-7	breast:
4	chr20:45985585..45987511-chr20:52689631..52691530,2	MCF-7	breast:
5	chr20:52682462..52684179-chr20:52688972..52691776,2	K562	blood:

Variant related genes	Relation type
BCAS1	TF binding region
ENSG00000202077	Chromatin interaction
ENSG00000174842	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000122484	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11699339	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13037207	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1531485	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1531486	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1537439	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1543703	0.88[YRI][hapmap]
rs290396	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs290440	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs290447	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3787547	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3787550	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs459376	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs460536	0.80[CHB][hapmap]
rs462041	0.90[CHB][hapmap]
rs462703	0.90[CHB][hapmap]
rs465096	0.85[CHB][hapmap]
rs6064045	0.83[MEX][hapmap]
rs6068765	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6068773	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6068774	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6068776	0.89[YRI][hapmap]
rs6512935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
3	nsv912944	chr20:52681759-52693614	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6064043	BCAS1	cis	lymphoblastoid	seeQTL
rs6064043	BCAS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52687200-52691600	Weak transcription	Gastric	stomach
2	chr20:52687400-52694000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr20:52687600-52691200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr20:52690000-52691000	Enhancers	Fetal Intestine Large	intestine
5	chr20:52690000-52692200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr20:52690000-52693400	Enhancers	Stomach Mucosa	stomach
7	chr20:52690400-52690800	Enhancers	Fetal Intestine Small	intestine
8	chr20:52690400-52690800	Bivalent Enhancer	HepG2	liver

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