Variant report

Variant	rs1499811
Chromosome Location	chr3:177425648-177425649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:177423921..177426469-chr3:177427048..177429863,3	K562	blood:
2	chr3:177424201..177426469-chr3:177427457..177429863,3	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10513747	0.99[ASN][1000 genomes]
rs10513748	0.81[ASN][1000 genomes]
rs10513749	0.84[CHB][hapmap]
rs10513750	0.84[CHB][hapmap]
rs10936953	0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs10936954	0.81[ASN][1000 genomes]
rs11915692	0.83[ASN][1000 genomes]
rs12487312	0.86[ASN][1000 genomes]
rs12487458	0.84[CHB][hapmap]
rs12489304	0.84[CHB][hapmap]
rs12489969	0.87[ASN][1000 genomes]
rs12496321	0.95[ASN][1000 genomes]
rs13059117	0.81[ASN][1000 genomes]
rs13059514	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs13064192	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13071785	0.86[ASN][1000 genomes]
rs13074455	0.97[ASN][1000 genomes]
rs13082519	0.84[CHB][hapmap]
rs13097562	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13097723	0.84[ASN][1000 genomes]
rs13098037	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1499809	0.95[ASN][1000 genomes]
rs1499810	0.86[ASN][1000 genomes]
rs1500047	0.83[ASN][1000 genomes]
rs1500048	0.97[ASN][1000 genomes]
rs1604032	0.81[ASN][1000 genomes]
rs17635512	0.95[ASN][1000 genomes]
rs17635597	0.97[ASN][1000 genomes]
rs1846628	0.83[ASN][1000 genomes]
rs2062499	0.84[CHB][hapmap]
rs2062500	0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs28700961	0.83[ASN][1000 genomes]
rs28711160	0.83[ASN][1000 genomes]
rs34066617	0.97[ASN][1000 genomes]
rs34188001	0.83[ASN][1000 genomes]
rs34347103	0.97[ASN][1000 genomes]
rs34407557	0.95[ASN][1000 genomes]
rs34491022	0.86[ASN][1000 genomes]
rs34557886	0.95[ASN][1000 genomes]
rs34638059	0.95[ASN][1000 genomes]
rs34763113	0.95[ASN][1000 genomes]
rs34992356	0.81[ASN][1000 genomes]
rs35110045	0.95[ASN][1000 genomes]
rs35468531	0.97[ASN][1000 genomes]
rs35610650	0.95[ASN][1000 genomes]
rs35652846	0.95[ASN][1000 genomes]
rs35830472	0.97[ASN][1000 genomes]
rs35847814	0.86[ASN][1000 genomes]
rs36055300	0.95[ASN][1000 genomes]
rs4857725	0.84[ASN][1000 genomes]
rs4857726	0.84[ASN][1000 genomes]
rs56005554	0.87[ASN][1000 genomes]
rs61541774	0.95[ASN][1000 genomes]
rs6443481	0.81[ASN][1000 genomes]
rs6443482	0.83[ASN][1000 genomes]
rs66636257	0.95[ASN][1000 genomes]
rs67189039	0.95[ASN][1000 genomes]
rs6765836	0.84[ASN][1000 genomes]
rs6772134	0.83[ASN][1000 genomes]
rs6779492	0.81[ASN][1000 genomes]
rs67797381	0.95[ASN][1000 genomes]
rs6793629	0.84[CHB][hapmap]
rs6793647	0.83[ASN][1000 genomes]
rs6798785	0.85[ASN][1000 genomes]
rs6803889	0.81[ASN][1000 genomes]
rs68151580	0.86[ASN][1000 genomes]
rs71308158	0.95[ASN][1000 genomes]
rs7615900	0.85[ASN][1000 genomes]
rs7639373	0.84[CHB][hapmap]
rs7644248	0.83[ASN][1000 genomes]
rs7646117	0.85[ASN][1000 genomes]
rs7652174	0.81[ASN][1000 genomes]
rs937507	0.81[ASN][1000 genomes]
rs937561	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv998537	chr3:177403421-177425648	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1013114	chr3:177421455-177443968	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1499811	SOX2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177413600-177432000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:177422200-177431800	Weak transcription	Aorta	Aorta
3	chr3:177424000-177426000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:177424600-177431400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:177425000-177429400	Weak transcription	Fetal Thymus	thymus
6	chr3:177425000-177431600	Weak transcription	Adipose Nuclei	Adipose
7	chr3:177425400-177427400	Weak transcription	Thymus	Thymus
8	chr3:177425400-177428000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:177425600-177428200	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:177425600-177432000	Weak transcription	Psoas Muscle	Psoas

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