Variant report

Variant	rs67426328
Chromosome Location	chr15:78934318-78934319
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:78933321-78934528	H1-hESC	embryonic stem cell:	n/a	chr15:78933390-78933400 chr15:78933626-78933636 chr15:78933915-78933924 chr15:78934500-78934509 chr15:78933914-78933923
2	MAX	chr15:78933630-78934340	H1-hESC	embryonic stem cell:	n/a	chr15:78933915-78933924 chr15:78933914-78933923
3	E2F6	chr15:78933405-78934363	H1-hESC	embryonic stem cell:	n/a	chr15:78933494-78933504 chr15:78933477-78933486
4	SIN3A	chr15:78932968-78934446	H1-hESC	embryonic stem cell:	n/a	chr15:78933607-78933620 chr15:78933171-78933184
5	GATA3	chr15:78934279-78934673	SH-SY5Y	brain:	n/a	chr15:78934460-78934467 chr15:78934460-78934469
6	JUND	chr15:78933422-78934448	H1-hESC	embryonic stem cell:	n/a	chr15:78933915-78933923 chr15:78933913-78933925 chr15:78933914-78933924 chr15:78933915-78933924 chr15:78933916-78933923 chr15:78933584-78933593
7	MAX	chr15:78933138-78934348	H1-hESC	embryonic stem cell:	n/a	chr15:78933249-78933259 chr15:78933390-78933400 chr15:78933626-78933636 chr15:78933915-78933924 chr15:78933914-78933923
8	GTF2F1	chr15:78933604-78934385	H1-hESC	embryonic stem cell:	n/a	n/a
9	GATA2	chr15:78934296-78935054	SH-SY5Y	brain:	n/a	chr15:78934460-78934467 chr15:78934460-78934469
10	RAD21	chr15:78933637-78934335	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr15:78933305-78934544	H1-hESC	embryonic stem cell:	n/a	chr15:78933494-78933504 chr15:78933384-78933394 chr15:78933477-78933486

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:78934280-78934330	GM06990	blood:	n/a
2	chr15:78934280-78934330	SK-N-SH_RA	brain:	n/a
3	chr15:78934280-78934330	HRCEpiC	kidney:	n/a
4	chr15:78934280-78934330	AG04449	skin:	fetal
5	chr15:78934280-78934330	U87	brain:	n/a
6	chr15:78934280-78934330	SAEC	small airway:	n/a
7	chr15:78934280-78934330	SK-N-SH	brain:	n/a
8	chr15:78934280-78934330	GM12878	blood:	n/a
9	chr15:78934280-78934330	GM19239	blood:	n/a
10	chr15:78934280-78934330	HUVEC	blood vessel:	n/a
11	chr15:78934280-78934330	CMK	blood:	n/a
12	chr15:78934280-78934330	HCT-116	colon:	n/a
13	chr15:78934280-78934330	HEEpiC	esophagus:	n/a
14	chr15:78934280-78934330	HRE	kidney:	n/a
15	chr15:78934280-78934330	HL-60	blood:	n/a
16	chr15:78934280-78934330	HRPEpiC	eye:	n/a
17	chr15:78934280-78934330	AG09309	skin:	n/a
18	chr15:78934280-78934330	ovcar-3	ovarian:	n/a
19	chr15:78934280-78934330	NHBE	bronchial:	n/a
20	chr15:78934280-78934330	MCF10A-Er-Src	breast:	n/a
21	chr15:78934280-78934330	HIPEpiC	eye:	n/a
22	chr15:78934280-78934330	PrEC	prostate:	n/a
23	chr15:78934280-78934330	BE2_C	brain:	n/a
24	chr15:78934280-78934330	NB4	blood:	n/a
25	chr15:78934280-78934330	NHDF-neo	bronchial:	n/a
26	chr15:78934280-78934330	AG09319	gingival:	n/a
27	chr15:78934280-78934330	Jurkat	blood:	n/a
28	chr15:78934280-78934330	Hepatocyte	liver:	n/a
29	chr15:78934280-78934330	AG04450	lung:	fetal
30	chr15:78934280-78934330	IMR90	lung:	fetal
31	chr15:78934280-78934330	HMEC	breast:	n/a
32	chr15:78934280-78934330	NH-A	brain:	n/a
33	chr15:78934280-78934330	HNPCEpiC	eye:	n/a
34	chr15:78934280-78934330	NT2-D1	testis:	n/a
35	chr15:78934280-78934330	RPTEC	kidney:	n/a
36	chr15:78934280-78934330	T-47D	breast:	n/a
37	chr15:78934280-78934330	ECC-1	luminal epithelium:	n/a
38	chr15:78934280-78934330	PFSK-1	brain:	n/a
39	chr15:78934280-78934330	GM12892	blood:	n/a
40	chr15:78934280-78934330	A549	lung:	n/a
41	chr15:78934280-78934330	Hela-S3	cervix:	n/a
42	chr15:78934280-78934330	HCM	heart:	n/a
43	chr15:78934280-78934330	HCPEpiC	choroid plexus:	n/a
44	chr15:78934280-78934330	GM12891	blood:	n/a
45	chr15:78934280-78934330	MCF-7	breast:	n/a
46	chr15:78934280-78934330	Caco-2	colon:	n/a
47	chr15:78934280-78934330	HCF	heart:	n/a
48	chr15:78934280-78934330	H1-hESC	embryonic stem cell:	embryo
49	chr15:78934280-78934330	HAEpiC	amniotic membrane:	n/a
50	chr15:78934280-78934330	HPAEpiC	pulmonary alveolar:	n/a

Variant related genes	Relation type
CHRNB4	TF binding region
CHRNB4	CpG island

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12902602	0.82[AFR][1000 genomes]
rs1996371	0.87[AFR][1000 genomes]
rs2869548	0.85[ASN][1000 genomes]
rs55988292	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743158	0.82[AMR][1000 genomes];0.93[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs67426328	CHRNA5	cis	Nerve Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78932600-78934400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr15:78932600-78935000	Enhancers	Fetal Brain Male	brain
3	chr15:78933000-78934400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr15:78933200-78934400	Bivalent Enhancer	Stomach Mucosa	stomach
5	chr15:78933400-78934600	Bivalent Enhancer	Placenta	Placenta
6	chr15:78933600-78934400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
7	chr15:78933600-78934400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr15:78933600-78937200	Weak transcription	Liver	Liver
9	chr15:78933800-78934400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:78933800-78934400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr15:78933800-78934400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:78933800-78934400	Enhancers	Primary B cells from peripheral blood	blood
13	chr15:78933800-78934400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr15:78933800-78934600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
15	chr15:78933800-78934600	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr15:78933800-78937200	Weak transcription	Psoas Muscle	Psoas
17	chr15:78933800-78960200	Weak transcription	Right Atrium	heart
18	chr15:78934000-78934400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:78934000-78934400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:78934000-78934400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr15:78934000-78934400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr15:78934000-78934400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:78934000-78934400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
24	chr15:78934000-78934400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr15:78934000-78934400	Bivalent Enhancer	Fetal Stomach	stomach
26	chr15:78934000-78934400	Enhancers	Stomach Smooth Muscle	stomach
27	chr15:78934000-78934600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
28	chr15:78934000-78934600	Enhancers	Primary T cells from cord blood	blood
29	chr15:78934000-78934600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr15:78934000-78934600	Enhancers	Fetal Thymus	thymus
31	chr15:78934000-78934600	Enhancers	K562	blood
32	chr15:78934000-78934800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr15:78934000-78934800	Enhancers	Thymus	Thymus
34	chr15:78934000-78936600	Weak transcription	Right Ventricle	heart
35	chr15:78934200-78934400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
36	chr15:78934200-78934400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr15:78934200-78934400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:78934200-78934600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr15:78934200-78934600	Enhancers	Fetal Brain Female	brain
40	chr15:78934200-78934800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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