Variant report

Variant	rs4390557
Chromosome Location	chr15:78717905-78717906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10519198	0.89[EUR][1000 genomes]
rs11072762	0.85[EUR][1000 genomes]
rs11072765	0.89[EUR][1000 genomes]
rs11639224	0.89[EUR][1000 genomes]
rs12899131	0.89[EUR][1000 genomes]
rs12909921	0.89[EUR][1000 genomes]
rs12910090	0.89[EUR][1000 genomes]
rs1847529	0.89[EUR][1000 genomes]
rs2036532	0.89[EUR][1000 genomes]
rs2568498	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2568500	0.89[EUR][1000 genomes]
rs2656058	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4436747	0.90[EUR][1000 genomes]
rs8041628	0.89[EUR][1000 genomes]
rs954144	0.87[EUR][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4390557	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs4390557	CHRNA3	cis	Muscle Skeletal	GTEx
rs4390557	RP11-650L12.2	cis	lung	GTEx
rs4390557	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs4390557	CHRNA5	cis	Esophagus Mucosa	GTEx
rs4390557	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs4390557	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs4390557	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs4390557	CHRNA5	cis	lung	GTEx
rs4390557	CHRNA5	cis	Nerve Tibial	GTEx
rs4390557	CHRNA5	cis	Heart Left Ventricle	GTEx
rs4390557	CHRNA5	cis	Muscle Skeletal	GTEx

Chromatin state (count:18 , 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	chr15:78712600-78718000	Weak transcription	Hela-S3	cervix
4	chr15:78713000-78718000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr15:78715000-78720800	Enhancers	Primary hematopoietic stem cells	blood
6	chr15:78715000-78721000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:78716400-78726200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:78717000-78719200	Enhancers	Dnd41	blood
9	chr15:78717200-78719000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:78717200-78719800	Weak transcription	K562	blood
11	chr15:78717400-78719200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr15:78717600-78718000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:78717600-78718800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:78717600-78718800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr15:78717600-78719000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr15:78717600-78719000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:78717800-78718000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr15:78717800-78718800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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