Variant report

Variant	rs2036532
Chromosome Location	chr15:78727386-78727387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10519198	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072762	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072765	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11639224	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12899131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910090	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1847529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568498	0.93[EUR][1000 genomes]
rs2568500	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2656058	0.93[EUR][1000 genomes]
rs2869046	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4390557	0.89[EUR][1000 genomes]
rs4436747	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8041628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs954144	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2036532	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs2036532	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs2036532	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs2036532	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs2036532	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs2036532	CHRNA5	cis	Heart Left Ventricle	GTEx
rs2036532	CHRNA5	cis	Nerve Tibial	GTEx
rs2036532	RP11-650L12.2	cis	lung	GTEx
rs2036532	CHRNA5	cis	Muscle Skeletal	GTEx

Chromatin state (count:13 , 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	chr15:78720800-78728400	Weak transcription	K562	blood
3	chr15:78725000-78729400	Weak transcription	Liver	Liver
4	chr15:78726400-78729600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:78726600-78727800	Enhancers	HepG2	liver
6	chr15:78726800-78729000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:78726800-78729400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr15:78726800-78729400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr15:78726800-78729600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:78726800-78729600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr15:78727000-78729400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:78727200-78729200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:78727200-78729600	Weak transcription	Rectal Mucosa Donor 31	rectum

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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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