Variant report

Variant	rs2936423
Chromosome Location	chr7:26948776-26948777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10081212	0.83[ASN][1000 genomes]
rs10242380	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10257437	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10257464	0.93[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259208	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10267689	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082312	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082315	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974418	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221446	0.88[EUR][1000 genomes]
rs17500459	1.00[ASN][1000 genomes]
rs1874924	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs213515	1.00[CEU][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213516	0.88[CEU][hapmap]
rs213518	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213521	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213533	0.94[CEU][hapmap]
rs213536	0.94[CEU][hapmap]
rs2140998	0.87[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34889704	1.00[ASN][1000 genomes]
rs477924	0.94[CEU][hapmap]
rs591895	0.94[CEU][hapmap]
rs6461982	0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs659131	0.93[CEU][hapmap]
rs6974705	1.00[ASN][1000 genomes]
rs774246	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774247	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774252	0.93[CEU][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774257	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774258	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774259	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774260	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774261	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774262	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774265	1.00[CEU][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774268	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776505	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7791056	0.93[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797624	1.00[ASN][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
rs2936423	HOTAIRM1	cis	Whole Blood	GTEx
rs2936423	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26943000-26949400	Weak transcription	HepG2	liver
2	chr7:26948200-26948800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:26948200-26950000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr7:26948200-26950400	Enhancers	NHEK	skin
5	chr7:26948400-26950400	Enhancers	HMEC	breast
6	chr7:26948400-26950400	Enhancers	HUVEC	blood vessel
7	chr7:26948400-26950600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:26948400-26950800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr7:26948600-26949200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:26948600-26950600	Enhancers	Hela-S3	cervix

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