Variant report

Variant	rs6495314
Chromosome Location	chr15:78960529-78960530
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1021071	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11072785	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11072790	0.88[EUR][1000 genomes]
rs11072791	0.85[EUR][1000 genomes]
rs11629637	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11633178	0.88[EUR][1000 genomes]
rs11634351	0.88[EUR][1000 genomes]
rs11634543	0.86[EUR][1000 genomes]
rs11638372	0.89[EUR][1000 genomes]
rs11638490	0.80[EUR][1000 genomes]
rs11638830	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11639049	0.83[EUR][1000 genomes]
rs11639166	0.83[EUR][1000 genomes]
rs11639181	0.83[EUR][1000 genomes]
rs11639347	0.83[EUR][1000 genomes]
rs11639372	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11639375	0.83[EUR][1000 genomes]
rs11639382	0.83[EUR][1000 genomes]
rs12286	0.84[CEU][hapmap]
rs12899135	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12901913	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12902602	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12910627	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs1809420	0.81[CEU][hapmap]
rs1825082	0.83[EUR][1000 genomes]
rs1825083	0.83[EUR][1000 genomes]
rs1996371	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2170311	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35583595	0.80[EUR][1000 genomes]
rs3813565	0.92[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap]
rs4886579	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4886580	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4887077	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4887082	0.88[CEU][hapmap]
rs60565501	0.87[ASN][1000 genomes]
rs7174367	0.81[CEU][hapmap]
rs72743199	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs922692	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv974713	chr15:78945824-78996783	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv457209	chr15:78949127-78986805	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv471256	chr15:78949127-78986805	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv570203	chr15:78949127-78986805	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6495314	PSMA4	cis	parietal	SCAN
rs6495314	CHRNA5	cis	parietal	SCAN
rs6495314	CHRNA5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78957000-78964200	Weak transcription	Fetal Kidney	kidney
2	chr15:78959200-78961000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr15:78959800-78960600	Enhancers	Left Ventricle	heart
4	chr15:78959800-78960600	Enhancers	Right Ventricle	heart
5	chr15:78959800-78960600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr15:78959800-78960800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr15:78959800-78960800	Enhancers	HepG2	liver
8	chr15:78960400-78960800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
9	chr15:78960400-78960800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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