Variant report

Variant	rs11638372
Chromosome Location	chr15:78983559-78983560
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	chr15:78977969..78980271-chr15:78982460..78985285,2	K562	blood:
2	chr15:78983381..78985912-chr15:78992265..78995147,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1021071	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051730	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11072785	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072790	0.95[EUR][1000 genomes]
rs11072791	0.91[EUR][1000 genomes]
rs11072792	0.86[EUR][1000 genomes]
rs11629637	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11630236	1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs11631955	1.00[JPT][hapmap]
rs11633178	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11634351	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11634543	0.92[EUR][1000 genomes]
rs11638490	0.85[EUR][1000 genomes]
rs11638830	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639044	0.84[MEX][hapmap];0.80[MKK][hapmap]
rs11639049	0.89[EUR][1000 genomes]
rs11639166	0.89[EUR][1000 genomes]
rs11639181	0.89[EUR][1000 genomes]
rs11639347	0.89[EUR][1000 genomes]
rs11639372	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639375	0.89[EUR][1000 genomes]
rs11639382	0.89[EUR][1000 genomes]
rs12286	0.96[CEU][hapmap]
rs12899135	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899147	0.84[MEX][hapmap]
rs12900168	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs12901913	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902602	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910627	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs16969968	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17487223	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs17487514	0.89[MKK][hapmap]
rs1809420	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap]
rs1825082	0.89[EUR][1000 genomes]
rs1825083	0.89[EUR][1000 genomes]
rs1994016	0.84[MEX][hapmap]
rs1996371	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036527	1.00[JPT][hapmap]
rs2170311	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2277550	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2869554	0.80[EUR][1000 genomes]
rs2869566	0.84[EUR][1000 genomes]
rs34225855	0.86[EUR][1000 genomes]
rs34563625	0.82[EUR][1000 genomes]
rs35583595	0.86[EUR][1000 genomes]
rs3813565	0.96[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4886579	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886580	0.93[EUR][1000 genomes]
rs4886587	0.82[EUR][1000 genomes]
rs4887077	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887082	1.00[CEU][hapmap]
rs4887086	0.83[EUR][1000 genomes]
rs4887087	0.84[EUR][1000 genomes]
rs6495314	0.89[EUR][1000 genomes]
rs7171916	0.81[CEU][hapmap]
rs7174367	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs7180002	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72743199	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031948	1.00[JPT][hapmap]
rs8034191	1.00[JPT][hapmap]
rs922692	0.99[AMR][1000 genomes];0.98[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
rs11638372	CHRNA5	cis	parietal	SCAN
rs11638372	CHRNA5	cis	cerebellum	SCAN
rs11638372	PSMA4	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78978400-78983600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:78978400-78984600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:78978400-78984600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:78978600-78983600	Weak transcription	Esophagus	oesophagus
5	chr15:78978600-78984000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:78978600-78985400	Weak transcription	Fetal Brain Female	brain
7	chr15:78978800-78983600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:78978800-78983600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr15:78978800-78983800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:78979000-78985000	Weak transcription	Thymus	Thymus
11	chr15:78979000-78988400	Weak transcription	Left Ventricle	heart
12	chr15:78979200-78983600	Weak transcription	Adipose Nuclei	Adipose
13	chr15:78979200-78983600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr15:78979200-78985000	Weak transcription	Fetal Thymus	thymus
15	chr15:78981400-78983600	Weak transcription	Gastric	stomach
16	chr15:78983200-78983800	Enhancers	Fetal Lung	lung
17	chr15:78983200-78984600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:78983200-78984600	Enhancers	Spleen	Spleen
19	chr15:78983200-78984800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr15:78983400-78984000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr15:78983400-78984000	Enhancers	Fetal Stomach	stomach
22	chr15:78983400-78984200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr15:78983400-78985200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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