Variant report

Variant	rs2494700
Chromosome Location	chr6:26631306-26631307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABT1-5	chr6:26630055-26634786	NONHSAT108301

Extended variants
information (count: 49 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1021372	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1021373	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1027203	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1027204	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13207371	0.84[EUR][1000 genomes]
rs1490488	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2130657	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2172007	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2451711	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2451712	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2451731	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2451740	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2451741	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2451744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2451750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2451751	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2494692	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2494701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2494709	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2494713	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2494716	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2498351	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2498380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504565	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2504566	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2504567	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2504571	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2758383	0.82[EUR][1000 genomes]
rs3001369	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34453863	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3800303	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4368798	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62394558	0.82[EUR][1000 genomes]
rs6925087	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7767847	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461273	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9461275	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461276	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9461288	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467802	0.81[ASN][1000 genomes]
rs9467804	0.82[ASN][1000 genomes]
rs9467805	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467810	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467813	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9467831	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2494700	RP11-457M11.2	cis	lung	GTEx
rs2494700	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs2494700	RP11-457M11.2	cis	Artery Tibial	GTEx
rs2494700	ZNF322	cis	Artery Tibial	GTEx
rs2494700	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs2494700	ZNF322	cis	Thyroid	GTEx
rs2494700	RP11-457M11.2	cis	Thyroid	GTEx
rs2494700	ZNF322	cis	Nerve Tibial	GTEx
rs2494700	ZNF322A	cis	multi-tissue	Pritchard
rs2494700	HCG11	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26625400-26639200	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:26629400-26639200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:26629600-26635400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:26629800-26631400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:26629800-26640000	Weak transcription	Left Ventricle	heart
6	chr6:26630400-26640000	Weak transcription	Aorta	Aorta
7	chr6:26630600-26633600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:26630800-26632800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:26631200-26631400	Active TSS	Gastric	stomach
10	chr6:26631200-26633000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:26631200-26633400	Weak transcription	HSMM	muscle
12	chr6:26631200-26633600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:26631200-26634000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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