Variant report

Variant	rs7162645
Chromosome Location	chr15:59993594-59993595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59991616..59994286-chr15:59995841..59997534,2	K562	blood:
2	chr15:59992550..59995081-chr15:59995698..59998010,2	MCF-7	breast:
3	chr15:59985971..59988155-chr15:59991640..59994225,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11629681	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634157	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12438078	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12439645	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12439658	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12439707	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440020	0.82[EUR][1000 genomes]
rs12442896	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12443242	0.82[EUR][1000 genomes]
rs12443297	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12904505	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12910451	0.82[EUR][1000 genomes]
rs17191002	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236867	0.82[EUR][1000 genomes]
rs1871504	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2306357	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs2306358	0.82[EUR][1000 genomes]
rs3087328	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs3843695	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3848119	0.83[EUR][1000 genomes]
rs3936513	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4775200	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56141740	0.82[EUR][1000 genomes]
rs6151440	0.82[EUR][1000 genomes]
rs6151441	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151442	0.81[EUR][1000 genomes]
rs6151444	0.82[EUR][1000 genomes]
rs6151445	0.82[EUR][1000 genomes]
rs6151446	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151447	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151448	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151449	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151450	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151451	0.81[EUR][1000 genomes]
rs6494138	0.82[EUR][1000 genomes]
rs6494139	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6494140	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173534	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7173827	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7178211	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs754642	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs754643	0.82[EUR][1000 genomes]
rs755605	0.82[EUR][1000 genomes]
rs8026404	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[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	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
3	nsv526682	chr15:59992758-59994943	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7162645	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59989000-59994000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:59989000-59994000	Weak transcription	K562	blood
3	chr15:59989800-59995000	Enhancers	NHEK	skin
4	chr15:59989800-59998400	Enhancers	Hela-S3	cervix
5	chr15:59992800-59993800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:59992800-59994000	Enhancers	A549	lung
7	chr15:59992800-59996800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:59993000-59994000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:59993000-59994000	Weak transcription	Stomach Mucosa	stomach
10	chr15:59993000-59998000	Weak transcription	HMEC	breast
11	chr15:59993200-59993600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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