Variant report

Variant	rs12438078
Chromosome Location	chr15:59988472-59988473
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59986007..59987827-chr15:59988230..59990878,2	MCF-7	breast:
2	chr15:59980286..59983504-chr15:59984854..59993428,11	K562	blood:
3	chr15:59981552..59983282-chr15:59987405..59989795,2	K562	blood:

Variant related genes	Relation type
ENSG00000259238	Chromatin interaction
ENSG00000140299	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11071471	0.86[EUR][1000 genomes]
rs11629681	0.88[EUR][1000 genomes]
rs11634157	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12439645	0.88[EUR][1000 genomes]
rs12439658	0.88[EUR][1000 genomes]
rs12439707	0.88[EUR][1000 genomes]
rs12440020	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12442896	0.82[EUR][1000 genomes]
rs12443242	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12443297	0.82[EUR][1000 genomes]
rs12904505	0.89[EUR][1000 genomes]
rs12910451	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17191002	0.88[EUR][1000 genomes]
rs17236867	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1871504	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs2306357	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2306358	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3087328	0.88[CEU][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3784389	0.95[JPT][hapmap]
rs3848119	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4775200	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs56141740	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151440	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151441	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151442	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151444	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151445	0.91[EUR][1000 genomes]
rs6151446	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151447	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151448	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs6151449	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs6151450	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs6151451	0.91[EUR][1000 genomes]
rs6494138	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6494139	0.83[EUR][1000 genomes]
rs6494140	0.89[EUR][1000 genomes]
rs7162645	0.89[EUR][1000 genomes]
rs7173534	0.83[EUR][1000 genomes]
rs7173827	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7178211	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs728037	0.89[EUR][1000 genomes]
rs728038	0.89[EUR][1000 genomes]
rs754641	0.88[EUR][1000 genomes]
rs754642	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs754643	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs755605	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8026404	0.96[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][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	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
2	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12438078	GTF2A2	cis	Whole Blood	GTEx
rs12438078	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59987000-59989800	Weak transcription	A549	lung
2	chr15:59987200-59989000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:59987200-59989800	Weak transcription	Hela-S3	cervix
4	chr15:59987400-59989000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:59988200-59989000	Enhancers	Fetal Intestine Large	intestine
6	chr15:59988200-59989000	Enhancers	K562	blood
7	chr15:59988400-59988800	Enhancers	Stomach Mucosa	stomach

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