Variant report

Variant	rs11639372
Chromosome Location	chr15:78966655-78966656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1021071	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051730	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11072785	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072790	0.90[EUR][1000 genomes]
rs11072791	0.87[EUR][1000 genomes]
rs11072792	0.81[EUR][1000 genomes]
rs11629637	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs11630236	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs11631955	1.00[JPT][hapmap]
rs11633178	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634351	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634543	0.88[EUR][1000 genomes]
rs11638372	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638490	0.81[EUR][1000 genomes]
rs11638830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639044	0.84[MEX][hapmap]
rs11639049	0.85[EUR][1000 genomes]
rs11639166	0.85[EUR][1000 genomes]
rs11639181	0.85[EUR][1000 genomes]
rs11639347	0.85[EUR][1000 genomes]
rs11639375	0.85[EUR][1000 genomes]
rs11639382	0.85[EUR][1000 genomes]
rs12286	0.85[CEU][hapmap]
rs12899135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899147	0.84[MEX][hapmap]
rs12900168	0.84[MEX][hapmap]
rs12901913	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902602	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910627	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs16969968	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17484524	1.00[JPT][hapmap]
rs17487223	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1809420	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs1825082	0.85[EUR][1000 genomes]
rs1825083	0.85[EUR][1000 genomes]
rs1994016	0.84[MEX][hapmap]
rs1996371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036527	1.00[JPT][hapmap]
rs2170311	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277550	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2869566	0.80[EUR][1000 genomes]
rs34225855	0.82[EUR][1000 genomes]
rs35583595	0.82[EUR][1000 genomes]
rs3813565	0.92[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4886579	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886580	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4887077	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887082	0.88[CEU][hapmap]
rs6495314	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7174367	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs7180002	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72743199	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031948	1.00[JPT][hapmap]
rs8034191	1.00[JPT][hapmap]
rs922692	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951266	1.00[CHB][hapmap];1.00[JPT][hapmap]

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
rs11639372	CHRNA5	cis	cerebellum	SCAN
rs11639372	PSMA4	cis	parietal	SCAN
rs11639372	CHRNA5	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78964000-78966800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr15:78964400-78972800	Weak transcription	Fetal Brain Female	brain
3	chr15:78965000-78968200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:78965000-78973200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:78965600-78968400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:78966000-78967400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:78966000-78968200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:78966200-78977000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:78966400-78967400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:78966600-78967200	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:78966600-78970000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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