Variant report

Variant	rs11857532
Chromosome Location	chr15:78968268-78968269
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1021071	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11072785	0.80[EUR][1000 genomes]
rs11638830	0.89[CEU][hapmap]
rs12899135	0.92[CEU][hapmap]
rs12902602	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1996371	0.89[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs3813565	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs4886579	0.80[AMR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11857532	CHRNA5	cis	parietal	SCAN
rs11857532	IREB2	cis	cerebellum	SCAN
rs11857532	CHRNA5	cis	cerebellum	SCAN
rs11857532	PSMA4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78964400-78972800	Weak transcription	Fetal Brain Female	brain
2	chr15:78965000-78973200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:78965600-78968400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:78966200-78977000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:78966600-78970000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:78966800-78969800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr15:78967400-78969400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:78967400-78970400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr15:78968000-78968600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
10	chr15:78968000-78969000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:78968200-78968400	Enhancers	H9 Cell Line	embryonic stem cell
12	chr15:78968200-78969200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr15:78968200-78969400	Enhancers	HUES48 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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