Variant report

Variant	rs3936513
Chromosome Location	chr15:60002601-60002602
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59990164..59992393-chr15:60002065..60004419,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11629681	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11634157	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12439645	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12439658	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439707	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12440020	0.84[EUR][1000 genomes]
rs12442896	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12443242	0.84[EUR][1000 genomes]
rs12443297	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12904505	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12910451	0.84[EUR][1000 genomes]
rs17191002	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17236867	0.83[EUR][1000 genomes]
rs1871503	0.81[AMR][1000 genomes]
rs1871504	0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1979423	0.80[AMR][1000 genomes]
rs2306357	0.84[EUR][1000 genomes]
rs2306358	0.84[EUR][1000 genomes]
rs3087328	0.84[EUR][1000 genomes]
rs3843695	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3848119	0.84[EUR][1000 genomes]
rs3912205	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3912206	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4775200	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56141740	0.84[EUR][1000 genomes]
rs6151440	0.84[EUR][1000 genomes]
rs6151441	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6151442	0.84[EUR][1000 genomes]
rs6151444	0.84[EUR][1000 genomes]
rs6151445	0.84[EUR][1000 genomes]
rs6151446	0.84[EUR][1000 genomes]
rs6151447	0.84[EUR][1000 genomes]
rs6151448	0.84[EUR][1000 genomes]
rs6151449	0.84[EUR][1000 genomes]
rs6151450	0.84[EUR][1000 genomes]
rs6151451	0.84[EUR][1000 genomes]
rs6151483	0.82[AMR][1000 genomes]
rs6151487	0.81[AMR][1000 genomes]
rs6151561	0.81[YRI][hapmap]
rs6494138	0.84[EUR][1000 genomes]
rs6494139	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6494140	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7162645	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7173534	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7173827	0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7178211	0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs728037	0.82[EUR][1000 genomes]
rs728038	0.82[EUR][1000 genomes]
rs754641	0.81[EUR][1000 genomes]
rs754642	0.84[EUR][1000 genomes]
rs754643	0.84[EUR][1000 genomes]
rs755605	0.84[EUR][1000 genomes]
rs8026404	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3936513	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL
rs3936513	GTF2A2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:60002200-60004800	Enhancers	Fetal Lung	lung
2	chr15:60002400-60002800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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