Variant report

Variant	rs1874924
Chromosome Location	chr7:26952902-26952903
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10242380	0.88[EUR][1000 genomes]
rs10257437	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10257464	0.93[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10259208	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10267689	0.88[EUR][1000 genomes]
rs1082312	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1082315	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11974418	0.88[EUR][1000 genomes]
rs11977871	0.81[CEU][hapmap]
rs12700785	0.83[ASW][hapmap]
rs13221446	0.88[EUR][1000 genomes]
rs213515	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs213516	0.94[CEU][hapmap]
rs213518	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs213521	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs213533	0.94[CEU][hapmap]
rs213536	0.94[CEU][hapmap]
rs2140998	0.87[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2693661	0.81[CEU][hapmap]
rs2936423	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs477924	0.94[CEU][hapmap]
rs591895	0.94[CEU][hapmap];0.81[GIH][hapmap]
rs6461982	0.96[YRI][hapmap]
rs659131	0.93[CEU][hapmap]
rs774246	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs774247	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs774252	0.93[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs774253	0.81[CEU][hapmap]
rs774257	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774258	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs774259	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs774260	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs774261	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774262	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774265	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs774268	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7776505	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7791056	0.93[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs954051	0.81[CEU][hapmap]

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	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1874924	HOXA2	Cis_1M	lymphoblastoid	RTeQTL
rs1874924	HOTAIRM1	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26950400-26956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:26950400-26957400	Weak transcription	NHEK	skin
3	chr7:26950400-26957600	Weak transcription	HMEC	breast
4	chr7:26950600-26958000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr7:26950600-26958400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:26951600-26953000	Enhancers	Fetal Lung	lung
7	chr7:26951600-26953000	Enhancers	Hela-S3	cervix
8	chr7:26951800-26953400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:26952000-26953600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr7:26952200-26953000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr7:26952200-26953200	Enhancers	Colon Smooth Muscle	Colon
12	chr7:26952200-26953600	Enhancers	Rectal Smooth Muscle	rectum
13	chr7:26952400-26955200	Weak transcription	Fetal Stomach	stomach

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