Variant report

Variant	rs503464
Chromosome Location	chr15:78857896-78857897
allele	A/T
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	POLR2A	chr15:78857447-78858282	MCF-7	breast:	n/a	n/a
2	RCOR1	chr15:78857527-78858870	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:78857554-78858281	HUVEC	blood vessel:	n/a	n/a
4	MAX	chr15:78857376-78858857	H1-hESC	embryonic stem cell:	n/a	chr15:78858584-78858594 chr15:78857648-78857658
5	MXI1	chr15:78857340-78858566	GM12878	blood:	n/a	n/a
6	MYC	chr15:78857826-78857980	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr15:78857705-78858386	NB4	blood:	n/a	n/a
8	YY1	chr15:78857828-78858241	GM12891	blood:	n/a	n/a
9	POLR2A	chr15:78857522-78858319	MCF-7	breast:	n/a	n/a
10	POLR2A	chr15:78857409-78858300	ECC-1	luminal epithelium:	n/a	n/a
11	MYC	chr15:78857777-78857963	MCF-7	breast:	n/a	n/a
12	MAX	chr15:78857447-78858385	HepG2	liver:	n/a	chr15:78857648-78857658
13	POLR2A	chr15:78857568-78858116	K562	blood:	n/a	n/a
14	POLR2A	chr15:78857671-78858428	MCF10A-Er-Src	breast:	n/a	n/a
15	IRF1	chr15:78857412-78858441	K562	blood:	n/a	chr15:78857810-78857824 chr15:78858309-78858323 chr15:78857758-78857772 chr15:78857720-78857734 chr15:78858184-78858198 chr15:78858309-78858322 chr15:78857832-78857846
16	POLR2A	chr15:78857697-78858140	K562	blood:	n/a	n/a
17	POLR2A	chr15:78857511-78858272	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr15:78857302-78859048	H1-hESC	embryonic stem cell:	n/a	n/a
19	TAF1	chr15:78857635-78857994	Hela-S3	cervix:	n/a	n/a
20	MYC	chr15:78857654-78858062	MCF-7	breast:	n/a	n/a
21	POLR2A	chr15:78857656-78858202	HepG2	liver:	n/a	n/a
22	POLR2A	chr15:78857716-78858268	A549	lung:	n/a	n/a
23	E2F6	chr15:78857346-78858661	H1-hESC	embryonic stem cell:	n/a	chr15:78857647-78857656 chr15:78857921-78857936 chr15:78858583-78858592 chr15:78857759-78857768
24	CREB1	chr15:78857676-78858363	A549	lung:	n/a	n/a
25	HA-E2F1	chr15:78857598-78858451	Hela-S3	cervix:	n/a	chr15:78857647-78857656 chr15:78857921-78857936 chr15:78857759-78857768
26	REST	chr15:78857731-78858033	A549	lung:	n/a	chr15:78857900-78857909 chr15:78857900-78857913 chr15:78857911-78857921
27	TAF1	chr15:78857660-78858032	PFSK-1	brain:	n/a	n/a
28	JUND	chr15:78857840-78858214	H1-hESC	embryonic stem cell:	n/a	chr15:78858189-78858198
29	TAF1	chr15:78857673-78858273	SK-N-SH	brain:	n/a	n/a
30	RFX5	chr15:78857510-78859006	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr15:78857706-78858105	U87	brain:	n/a	n/a
32	CTCF	chr15:78857860-78858010	GM12865	blood:	n/a	chr15:78857877-78857890
33	MAX	chr15:78857780-78858201	HepG2	liver:	n/a	n/a
34	TAF1	chr15:78857697-78858332	H1-hESC	embryonic stem cell:	n/a	n/a
35	SP1	chr15:78857438-78858716	A549	lung:	n/a	chr15:78858185-78858194 chr15:78857833-78857843 chr15:78857834-78857843 chr15:78858186-78858195 chr15:78857726-78857736 chr15:78857726-78857735 chr15:78857812-78857821 chr15:78857720-78857731 chr15:78857833-78857843 chr15:78857646-78857657 chr15:78857725-78857737 chr15:78857810-78857822 chr15:78857811-78857821 chr15:78858181-78858195 chr15:78857647-78857656 chr15:78857758-78857770 chr15:78857722-78857731 chr15:78857832-78857844 chr15:78857727-78857736 chr15:78857832-78857844 chr15:78857646-78857658 chr15:78857727-78857736 chr15:78858184-78858196 chr15:78857810-78857822 chr15:78857834-78857843 chr15:78857643-78857657 chr15:78857758-78857770 chr15:78858185-78858195 chr15:78857725-78857737 chr15:78857760-78857769 chr15:78858189-78858201 chr15:78858185-78858195 chr15:78858184-78858196 chr15:78857759-78857768 chr15:78857720-78857732 chr15:78858186-78858195 chr15:78857833-78857842 chr15:78858591-78858605
36	MXI1	chr15:78857509-78858727	Hela-S3	cervix:	n/a	n/a
37	HDAC2	chr15:78857307-78858701	MCF-7	breast:	n/a	n/a
38	CEBPB	chr15:78857622-78858185	Hela-S3	cervix:	n/a	n/a
39	TAF1	chr15:78857760-78858052	K562	blood:	n/a	n/a
40	EP300	chr15:78857311-78858098	K562	blood:	n/a	n/a
41	POLR2A	chr15:78857124-78858298	GM19193	blood:	n/a	n/a
42	E2F1	chr15:78857676-78858384	Hela-S3	cervix:	n/a	chr15:78857921-78857936 chr15:78857759-78857768
43	MYC	chr15:78857629-78858098	MCF10A-Er-Src	breast:	n/a	chr15:78857648-78857658
44	POLR2A	chr15:78857426-78858032	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:78857259-78858189	GM12878	blood:	n/a	n/a
46	ZNF143	chr15:78857545-78858056	GM12878	blood:	n/a	chr15:78857745-78857763
47	EP300	chr15:78857877-78858075	HepG2	liver:	n/a	n/a
48	POLR2A	chr15:78857745-78858363	H1-hESC	embryonic stem cell:	n/a	n/a
49	ELF1	chr15:78857739-78858346	GM12878	blood:	n/a	n/a
50	CHD2	chr15:78857573-78858804	Hela-S3	cervix:	n/a	chr15:78858186-78858196 chr15:78857727-78857737

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:78857848-78857898	GM06990	blood:	n/a
2	chr15:78857848-78857898	Jurkat	blood:	n/a
3	chr15:78857848-78857898	GM12878	blood:	n/a
4	chr15:78857848-78857898	GM12891	blood:	n/a
5	chr15:78857848-78857898	CMK	blood:	n/a
6	chr15:78857848-78857898	HRPEpiC	eye:	n/a
7	chr15:78857848-78857898	MCF10A-Er-Src	breast:	n/a
8	chr15:78857848-78857898	MCF-7	breast:	n/a
9	chr15:78857848-78857898	HCF	heart:	n/a
10	chr15:78857848-78857898	A549	lung:	n/a
11	chr15:78857848-78857898	NB4	blood:	n/a
12	chr15:78857848-78857898	HepG2	liver:	n/a
13	chr15:78857848-78857898	HRE	kidney:	n/a
14	chr15:78857848-78857898	HCM	heart:	n/a
15	chr15:78857848-78857898	ECC-1	luminal epithelium:	n/a
16	chr15:78857848-78857898	U87	brain:	n/a
17	chr15:78857848-78857898	PrEC	prostate:	n/a
18	chr15:78857848-78857898	ProgFib	skin:	n/a
19	chr15:78857848-78857898	AG09309	skin:	n/a
20	chr15:78857848-78857898	GM12892	blood:	n/a
21	chr15:78857848-78857898	HIPEpiC	eye:	n/a
22	chr15:78857848-78857898	Hepatocyte	liver:	n/a
23	chr15:78857848-78857898	NT2-D1	testis:	n/a
24	chr15:78857848-78857898	HUVEC	blood vessel:	n/a
25	chr15:78857848-78857898	GM19239	blood:	n/a
26	chr15:78857848-78857898	PFSK-1	brain:	n/a
27	chr15:78857848-78857898	NHDF-neo	bronchial:	n/a
28	chr15:78857848-78857898	AG10803	skin:	n/a
29	chr15:78857848-78857898	AoSMC	blood vessel:	n/a
30	chr15:78857848-78857898	HCPEpiC	choroid plexus:	n/a
31	chr15:78857848-78857898	H1-hESC	embryonic stem cell:	embryo
32	chr15:78857848-78857898	SAEC	small airway:	n/a
33	chr15:78857848-78857898	NHBE	bronchial:	n/a
34	chr15:78857848-78857898	AG09319	gingival:	n/a
35	chr15:78857848-78857898	HNPCEpiC	eye:	n/a
36	chr15:78857848-78857898	NH-A	brain:	n/a
37	chr15:78857848-78857898	Hela-S3	cervix:	n/a
38	chr15:78857848-78857898	HMEC	breast:	n/a
39	chr15:78857848-78857898	SK-N-SH	brain:	n/a
40	chr15:78857848-78857898	HAEpiC	amniotic membrane:	n/a
41	chr15:78857848-78857898	BE2_C	brain:	n/a
42	chr15:78857848-78857898	PANC-1	pancreas:	n/a
43	chr15:78857848-78857898	HPAEpiC	pulmonary alveolar:	n/a
44	chr15:78857848-78857898	RPTEC	kidney:	n/a
45	chr15:78857848-78857898	HL-60	blood:	n/a
46	chr15:78857848-78857898	HEEpiC	esophagus:	n/a
47	chr15:78857848-78857898	SKMC	muscle:	n/a
48	chr15:78857848-78857898	Caco-2	colon:	n/a
49	chr15:78857848-78857898	SK-N-MC	brain:	n/a
50	chr15:78857848-78857898	T-47D	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78799175..78801434-chr15:78856957..78860049,3	K562	blood:
2	chr15:78857388..78857943-chr17:41465368..41466133,2	Hela-S3	cervix:
3	chr15:78829726..78832334-chr15:78857099..78858875,2	K562	blood:
4	chr15:78829726..78834442-chr15:78855710..78860360,8	K562	blood:
5	chr15:78856926..78859657-chr19:33792449..33795095,2	MCF-7	breast:
6	chr15:78832604..78836535-chr15:78856473..78859290,6	MCF-7	breast:
7	chr15:78857563..78858250-chr20:30192805..30193555,2	Hela-S3	cervix:
8	chr15:78773415..78776394-chr15:78857535..78859504,2	MCF-7	breast:
9	chr15:75743021..75745154-chr15:78857416..78860250,2	MCF-7	breast:
10	chr1:148241054..148241820-chr15:78857641..78858374,2	Hela-S3	cervix:
11	chr15:78831297..78836398-chr15:78856605..78860226,12	MCF-7	breast:
12	chr15:78785104..78787346-chr15:78855967..78858154,2	MCF-7	breast:
13	chr15:78856606..78859221-chr15:78887185..78889989,2	MCF-7	breast:
14	chr12:1099424..1099985-chr15:78857604..78858376,2	Hela-S3	cervix:
15	chr1:28974756..28975416-chr15:78857639..78858148,2	Hela-S3	cervix:
16	chr15:78832891..78834488-chr15:78856612..78858995,2	K562	blood:

Variant related genes	Relation type
CHRNA5	TF binding region
CHRNA5	CpG island
ENSG00000041357	Chromatin interaction
ENSG00000259474	Chromatin interaction
ENSG00000267296	Chromatin interaction
ENSG00000178863	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000136381	Chromatin interaction
ENSG00000250132	Chromatin interaction
ENSG00000082805	Chromatin interaction
ENSG00000169375	Chromatin interaction
ENSG00000080644	Chromatin interaction
ENSG00000245848	Chromatin interaction
ENSG00000207501	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000230259	Chromatin interaction
ENSG00000188266	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000268838	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12438181	0.83[EUR][1000 genomes]
rs12438659	0.83[EUR][1000 genomes]
rs12439240	0.88[EUR][1000 genomes]
rs12441354	0.83[EUR][1000 genomes]
rs12441426	0.83[EUR][1000 genomes]
rs2036534	0.83[EUR][1000 genomes]
rs28395178	0.80[EUR][1000 genomes]
rs28437878	0.83[EUR][1000 genomes]
rs28498264	0.87[EUR][1000 genomes]
rs34138960	0.87[EUR][1000 genomes]
rs34664138	0.87[EUR][1000 genomes]
rs35212593	0.87[EUR][1000 genomes]
rs3813570	0.85[EUR][1000 genomes]
rs4461039	0.83[EUR][1000 genomes]
rs569207	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57064725	0.81[EUR][1000 genomes]
rs576982	0.83[ASN][1000 genomes]
rs59133824	0.87[EUR][1000 genomes]
rs59683676	0.87[EUR][1000 genomes]
rs61204066	0.84[EUR][1000 genomes]
rs637137	0.85[ASN][1000 genomes]
rs667282	0.85[ASN][1000 genomes]
rs684513	0.84[EUR][1000 genomes]
rs7163730	0.84[EUR][1000 genomes]
rs7169584	0.83[EUR][1000 genomes]
rs7173514	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181245	0.83[EUR][1000 genomes]
rs7181447	0.83[EUR][1000 genomes]
rs905739	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs503464	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs503464	CHRNA5	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78856800-78859400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr15:78857200-78858000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:78857200-78858000	Flanking Active TSS	Dnd41	blood
4	chr15:78857200-78858200	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr15:78857200-78858200	Active TSS	Brain Germinal Matrix	brain
6	chr15:78857200-78858200	Enhancers	Placenta	Placenta
7	chr15:78857200-78858200	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr15:78857200-78859400	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr15:78857200-78859400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:78857400-78858000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
11	chr15:78857400-78858000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:78857400-78858000	Active TSS	Psoas Muscle	Psoas
13	chr15:78857400-78858200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:78857400-78858200	Active TSS	Brain Anterior Caudate	brain
15	chr15:78857400-78858200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
16	chr15:78857400-78858400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:78857400-78858400	Active TSS	Muscle Satellite Cultured Cells	--
18	chr15:78857400-78858400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:78857400-78858400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
20	chr15:78857400-78858400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:78857400-78858400	Active TSS	Brain Substantia Nigra	brain
22	chr15:78857400-78858400	Active TSS	Right Ventricle	heart
23	chr15:78857400-78858400	Active TSS	Stomach Smooth Muscle	stomach
24	chr15:78857400-78858400	Active TSS	HSMM	muscle
25	chr15:78857400-78858400	Active TSS	NH-A	brain
26	chr15:78857400-78858600	Active TSS	Colon Smooth Muscle	Colon
27	chr15:78857400-78858600	Active TSS	Ovary	ovary
28	chr15:78857400-78858800	Active TSS	Aorta	Aorta
29	chr15:78857400-78858800	Flanking Active TSS	Thymus	Thymus
30	chr15:78857400-78859000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr15:78857400-78859000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:78857400-78859000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:78857400-78859000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
34	chr15:78857400-78859200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr15:78857400-78859200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:78857400-78859200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:78857400-78859200	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr15:78857400-78859200	Active TSS	Fetal Kidney	kidney
39	chr15:78857400-78859400	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr15:78857600-78858000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr15:78857600-78858000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr15:78857600-78858200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:78857600-78858200	Active TSS	Primary B cells from peripheral blood	blood
44	chr15:78857600-78858200	Active TSS	Primary T cells from cord blood	blood
45	chr15:78857600-78858200	Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr15:78857600-78858200	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr15:78857600-78858200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:78857600-78858200	Active TSS	Adipose Nuclei	Adipose
49	chr15:78857600-78858200	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr15:78857600-78858200	Active TSS	Skeletal Muscle Female	skeletal muscle

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