Variant report

Variant	rs1188177
Chromosome Location	chr14:56446044-56446045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1188164	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1188165	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1188167	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1188168	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1188169	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1188170	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1188171	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1188172	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1188173	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1188178	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1188182	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1188183	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1188189	0.81[ASN][1000 genomes]
rs1188195	0.81[ASN][1000 genomes]
rs1188201	0.88[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs1188202	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1188205	0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs8015854	0.93[ASN][1000 genomes]
rs922653	0.83[ASN][1000 genomes]
rs922654	0.83[ASN][1000 genomes]
rs922656	0.85[ASN][1000 genomes]
rs966880	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	nsv901977	chr14:56213392-56492996	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv34106	chr14:56346245-56550642	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1188177	SAMD4A	cis	parietal	SCAN
rs1188177	RPS5	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56439200-56451200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:56440000-56446200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr14:56440000-56446400	Enhancers	Brain Germinal Matrix	brain
4	chr14:56442800-56446600	Enhancers	Brain Substantia Nigra	brain
5	chr14:56443000-56446400	Enhancers	Brain Cingulate Gyrus	brain
6	chr14:56443600-56446200	Enhancers	Brain Anterior Caudate	brain
7	chr14:56443600-56446400	Enhancers	Brain Hippocampus Middle	brain
8	chr14:56443600-56446600	Enhancers	Brain Angular Gyrus	brain
9	chr14:56444800-56449200	Weak transcription	Ovary	ovary
10	chr14:56445600-56446200	Enhancers	Cortex derived primary cultured neurospheres	brain

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