Variant report

Variant	rs6494139
Chromosome Location	chr15:59992164-59992165
allele	A/C
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	chr15:59980286..59982488-chr15:59991849..59993428,2	K562	blood:
3	chr15:59980286..59983504-chr15:59984854..59993428,11	K562	blood:
4	chr15:59990164..59992393-chr15:60002065..60004419,2	MCF-7	breast:
5	chr15:59985971..59988155-chr15:59991640..59994225,2	K562	blood:

Variant related genes	Relation type
ENSG00000140299	Chromatin interaction
ENSG00000259238	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11071471	0.83[EUR][1000 genomes]
rs11629681	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11634157	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12438078	0.83[EUR][1000 genomes]
rs12439645	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12439658	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12439707	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12440020	0.89[EUR][1000 genomes]
rs12442896	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443242	0.89[EUR][1000 genomes]
rs12443297	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12904505	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12910451	0.89[EUR][1000 genomes]
rs17191002	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1871503	0.82[AMR][1000 genomes]
rs1871504	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2306357	0.89[EUR][1000 genomes]
rs2306358	0.89[EUR][1000 genomes]
rs3087328	0.89[EUR][1000 genomes]
rs3843695	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3912205	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3912206	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3936513	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775200	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56141740	0.89[EUR][1000 genomes]
rs6151440	0.89[EUR][1000 genomes]
rs6151441	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6151442	0.89[EUR][1000 genomes]
rs6151444	0.89[EUR][1000 genomes]
rs6151445	0.89[EUR][1000 genomes]
rs6151446	0.89[EUR][1000 genomes]
rs6151447	0.89[EUR][1000 genomes]
rs6151448	0.89[EUR][1000 genomes]
rs6151449	0.89[EUR][1000 genomes]
rs6151450	0.89[EUR][1000 genomes]
rs6151451	0.89[EUR][1000 genomes]
rs6151483	0.81[AMR][1000 genomes]
rs6151487	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6494138	0.89[EUR][1000 genomes]
rs6494140	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7162645	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7173534	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173827	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178211	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728037	0.87[EUR][1000 genomes]
rs728038	0.87[EUR][1000 genomes]
rs754641	0.86[EUR][1000 genomes]
rs754642	0.89[EUR][1000 genomes]
rs754643	0.89[EUR][1000 genomes]
rs755605	0.89[EUR][1000 genomes]
rs8026404	0.82[AMR][1000 genomes];0.89[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
rs6494139	GTF2A2	cis	Whole Blood	GTEx
rs6494139	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59988800-59992200	Weak transcription	Stomach Mucosa	stomach
2	chr15:59989000-59992200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:59989000-59994000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:59989000-59994000	Weak transcription	K562	blood
5	chr15:59989800-59995000	Enhancers	NHEK	skin
6	chr15:59989800-59998400	Enhancers	Hela-S3	cervix
7	chr15:59990200-59992200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:59990400-59992200	Weak transcription	HMEC	breast
9	chr15:59991600-59993000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:59991600-59993000	Enhancers	HUVEC	blood vessel
11	chr15:59992000-59992800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:59992000-59992800	Flanking Active TSS	A549	lung

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