Variant report

Variant	rs1948
Chromosome Location	chr15:78917399-78917400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs2904130	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3743073	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs3743074	0.91[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs3743075	0.91[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs4887070	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62010332	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6495309	0.86[JPT][hapmap]
rs8023462	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv570202	chr15:78915245-78953785	Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1948	CHRNA3	cis	Muscle Skeletal	GTEx
rs1948	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs1948	CHRNA5	cis	lung	GTEx
rs1948	CHRNA3	cis	parietal	SCAN
rs1948	IREB2	cis	cerebellum	SCAN
rs1948	CHRNA5	cis	Esophagus Mucosa	GTEx
rs1948	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs1948	CHRNA5	cis	parietal	SCAN
rs1948	CHRNA5	cis	Nerve Tibial	GTEx
rs1948	CHRNA5	cis	Muscle Skeletal	GTEx
rs1948	CHRNA5	cis	cerebellum	SCAN
rs1948	FAH	cis	parietal	SCAN
rs1948	RP11-650L12.2	cis	lung	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78914800-78921600	Enhancers	Fetal Thymus	thymus
2	chr15:78915000-78917400	Enhancers	Thymus	Thymus
3	chr15:78915000-78929600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:78916600-78918200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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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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