Variant report

Variant	rs1999349
Chromosome Location	chr9:110670409-110670410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:110666092..110668154-chr9:110669795..110672142,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10739249	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10759262	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10759264	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10759265	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759266	0.90[ASN][1000 genomes]
rs10816585	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10816586	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13293417	0.81[AFR][1000 genomes]
rs1339764	0.81[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1339765	0.90[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1416839	0.82[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1929277	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1929279	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1929280	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1970403	0.89[ASN][1000 genomes]
rs2039802	0.87[MKK][hapmap];0.82[YRI][hapmap]
rs2094919	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2094920	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2104825	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4978644	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4978650	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4978651	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7023709	0.90[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7030786	0.82[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7031148	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7040902	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7047831	0.90[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs7853326	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7858147	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7873668	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs944473	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs944475	0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs944476	0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][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	nsv1051101	chr9:110548257-110697253	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv893701	chr9:110650482-110709587	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1999349	CHRNA1	trans	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110666800-110670800	Enhancers	Fetal Muscle Leg	muscle
2	chr9:110667000-110671000	Enhancers	Brain Cingulate Gyrus	brain
3	chr9:110668800-110672200	Weak transcription	Psoas Muscle	Psoas
4	chr9:110669400-110671000	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr9:110670000-110670600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:110670000-110670600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:110670000-110670600	Active TSS	Brain Substantia Nigra	brain
8	chr9:110670200-110670800	Enhancers	Brain Angular Gyrus	brain
9	chr9:110670400-110670800	Active TSS	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links