Variant report

Variant	rs2017295
Chromosome Location	chr15:79033269-79033270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1045130	0.86[AMR][1000 genomes]
rs12901331	0.84[ASN][1000 genomes]
rs12906171	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1964562	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2005263	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046143	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34019568	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34067845	0.84[ASN][1000 genomes]
rs34099810	0.84[ASN][1000 genomes]
rs34422348	0.84[ASN][1000 genomes]
rs34552906	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs35602248	0.81[AMR][1000 genomes]
rs35741852	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs59414039	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67775542	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2017295	CHRNA3	cis	Muscle Skeletal	GTEx
rs2017295	CHRNA5	cis	Muscle Skeletal	GTEx
rs2017295	RP11-650L12.2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79031800-79033800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:79032600-79033400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:79032600-79033400	Enhancers	Gastric	stomach
4	chr15:79032600-79033600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr15:79032600-79034000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr15:79032800-79033400	Enhancers	Spleen	Spleen
7	chr15:79033000-79033400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:79033000-79033400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr15:79033000-79045000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:79033200-79033400	Bivalent Enhancer	K562	blood
11	chr15:79033200-79033600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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Input of quick search could be:

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

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