Variant report

Variant	rs8004777
Chromosome Location	chr14:32958979-32958980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr14:32958971-32959171	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
AKAP6	TF binding region
ENSG00000259045	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10130278	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10130375	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10130385	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10131325	0.91[EUR][1000 genomes]
rs10131652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10141239	0.81[AMR][1000 genomes]
rs10143760	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10143778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12147858	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12232175	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1951197	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1951198	0.96[ASN][1000 genomes]
rs1951199	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1951200	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1951201	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1957031	0.96[ASN][1000 genomes]
rs1957032	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1957033	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1957034	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1957035	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1957036	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1961349	0.84[EUR][1000 genomes]
rs2383333	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3784196	0.85[ASN][1000 genomes]
rs4296166	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4332665	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353399	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4427713	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4433719	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4489913	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4981155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981156	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4981972	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4981973	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4981974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7160547	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7492909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8004271	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8004563	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8005075	0.80[EUR][1000 genomes]
rs8005890	0.85[EUR][1000 genomes]
rs8006554	0.81[EUR][1000 genomes]
rs8010095	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8010225	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8014556	0.80[EUR][1000 genomes]
rs941750	0.85[ASN][1000 genomes]
rs941751	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758352	chr14:32858480-33016442	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2759978	chr14:32858480-33016442	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv901595	chr14:32928634-32961434	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv974324	chr14:32950342-32961052	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8004777	RALGAPA1	cis	cerebellum	SCAN
rs8004777	KIAA0391	cis	cerebellum	SCAN
rs8004777	COCH	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:32947600-32962200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr14:32947800-32960600	Weak transcription	Fetal Brain Male	brain
3	chr14:32947800-32963400	Weak transcription	Right Atrium	heart
4	chr14:32950800-32960600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:32951400-32960600	Weak transcription	Left Ventricle	heart
6	chr14:32951600-32960600	Weak transcription	Brain Substantia Nigra	brain
7	chr14:32951800-32960200	Weak transcription	Fetal Heart	heart
8	chr14:32957800-32961800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr14:32957800-32963000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr14:32957800-32963200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:32958200-32962400	Weak transcription	Right Ventricle	heart
12	chr14:32958400-32961200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr14:32958600-32962400	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links