Variant report

Variant	rs11071471
Chromosome Location	chr15:59984882-59984883
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59981348..59983178-chr15:59984854..59987246,2	K562	blood:
2	chr15:59982442..59985079-chr15:60617660..60619822,3	K562	blood:
3	chr15:59980286..59983504-chr15:59984854..59993428,11	K562	blood:
4	chr15:59982661..59985453-chr15:60307670..60309447,2	K562	blood:

Variant related genes	Relation type
ENSG00000140299	Chromatin interaction
ENSG00000259238	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12438078	0.86[EUR][1000 genomes]
rs12440020	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12442896	0.82[EUR][1000 genomes]
rs12443242	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12443297	0.84[EUR][1000 genomes]
rs12910451	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17236804	0.80[ASN][1000 genomes]
rs1871504	0.83[EUR][1000 genomes]
rs2306357	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306358	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2307275	0.80[ASN][1000 genomes]
rs3087328	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4533213	0.80[ASN][1000 genomes]
rs56141740	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151440	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151441	0.83[EUR][1000 genomes]
rs6151442	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151444	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151445	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151446	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151447	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151448	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151449	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151450	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151451	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6151458	0.83[ASN][1000 genomes]
rs6151460	0.83[ASN][1000 genomes]
rs6151461	0.83[ASN][1000 genomes]
rs6151462	0.82[ASN][1000 genomes]
rs6151467	0.83[ASN][1000 genomes]
rs6151470	0.83[ASN][1000 genomes]
rs6151472	0.82[ASN][1000 genomes]
rs6151474	0.82[ASN][1000 genomes]
rs6151477	0.81[ASN][1000 genomes]
rs6151486	0.80[ASN][1000 genomes]
rs6151491	0.80[ASN][1000 genomes]
rs6151494	0.80[ASN][1000 genomes]
rs6151496	0.80[ASN][1000 genomes]
rs6151501	0.81[ASN][1000 genomes]
rs6494138	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6494139	0.83[EUR][1000 genomes]
rs67712565	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7173534	0.83[EUR][1000 genomes]
rs7173827	0.83[EUR][1000 genomes]
rs7178211	0.83[EUR][1000 genomes]
rs722163	0.83[ASN][1000 genomes]
rs722164	0.83[ASN][1000 genomes]
rs728037	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs728038	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs754641	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs754642	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs754643	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs755605	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11071471	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL
rs11071471	GTF2A2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59982200-59986600	Weak transcription	Stomach Mucosa	stomach
2	chr15:59982600-59987200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:59982800-59986400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:59983200-59986800	Weak transcription	Fetal Intestine Large	intestine
5	chr15:59983400-59985000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr15:59983600-59985200	Weak transcription	Hela-S3	cervix
7	chr15:59983600-59986800	Weak transcription	A549	lung
8	chr15:59984200-59985200	Weak transcription	Liver	Liver

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