Variant report

Variant	rs2869046
Chromosome Location	chr15:78720966-78720967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10519198	0.86[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11072762	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072763	0.84[ASN][1000 genomes]
rs11072765	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11639224	0.86[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12899131	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12909921	0.86[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12910090	0.83[JPT][hapmap];0.85[AMR][1000 genomes]
rs1847529	0.86[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2036532	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2869030	0.90[JPT][hapmap]
rs4436747	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8041628	0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs954144	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	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
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1627	chr15:78683761-78728604	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2869046	CHRNA5	cis	Nerve Tibial	GTEx
rs2869046	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs2869046	CHRNA5	cis	Heart Left Ventricle	GTEx
rs2869046	CHRNA5	cis	Muscle Skeletal	GTEx
rs2869046	RP11-650L12.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78698200-78729800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78700800-78722000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:78715000-78721000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:78716400-78726200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:78718800-78721000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:78719800-78721000	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr15:78720800-78721400	Weak transcription	HepG2	liver
8	chr15:78720800-78722400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr15:78720800-78726400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr15:78720800-78728400	Weak transcription	K562	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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