Variant report

Variant	rs7173827
Chromosome Location	chr15:59992337-59992338
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	chr15:59980286..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
ENSG00000259238	Chromatin interaction
ENSG00000140299	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11071471	0.83[EUR][1000 genomes]
rs11629681	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11634157	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12438078	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12439645	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12439658	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12439707	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12440020	0.89[EUR][1000 genomes]
rs12442896	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443242	0.89[EUR][1000 genomes]
rs12443297	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12904505	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12910451	0.89[EUR][1000 genomes]
rs17191002	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1871499	0.81[JPT][hapmap];0.90[YRI][hapmap]
rs1871503	0.81[AMR][1000 genomes]
rs1871504	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2101019	0.89[YRI][hapmap]
rs2306354	0.81[YRI][hapmap]
rs2306357	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2306358	0.89[EUR][1000 genomes]
rs2307273	0.90[JPT][hapmap]
rs2899649	0.89[JPT][hapmap];0.92[YRI][hapmap]
rs3087328	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs3825870	0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs3843695	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3912205	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3912206	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3936513	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4270113	0.90[JPT][hapmap];0.89[YRI][hapmap]
rs4775200	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56141740	0.89[EUR][1000 genomes]
rs6151440	0.89[EUR][1000 genomes]
rs6151441	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[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	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6151447	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6151448	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6151449	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6151450	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6151451	0.89[EUR][1000 genomes]
rs6151483	0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs6151487	0.81[AMR][1000 genomes]
rs6151510	0.91[JPT][hapmap];0.87[YRI][hapmap]
rs6151525	0.90[JPT][hapmap]
rs6151551	0.90[JPT][hapmap]
rs6151553	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs6151561	0.89[JPT][hapmap];0.93[YRI][hapmap]
rs6494138	0.89[EUR][1000 genomes]
rs6494139	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494140	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7162645	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7173534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[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	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs754643	0.89[EUR][1000 genomes]
rs755605	0.89[EUR][1000 genomes]
rs7882	1.00[JPT][hapmap];0.93[YRI][hapmap]
rs8026404	0.88[CEU][hapmap];0.83[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
rs7173827	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL
rs7173827	GTF2A2	cis	Whole Blood	GTEx

Chromatin state (count:13 , 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	chr15:59991600-59993000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:59991600-59993000	Enhancers	HUVEC	blood vessel
7	chr15:59992000-59992800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:59992000-59992800	Flanking Active TSS	A549	lung
9	chr15:59992200-59992800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:59992200-59993000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:59992200-59993000	Enhancers	Stomach Mucosa	stomach
12	chr15:59992200-59993000	Enhancers	HMEC	breast
13	chr15:59992200-59993200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links