Variant report

Variant	rs3809393
Chromosome Location	chr14:69446113-69446114
allele	A/C
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	CEBPB	chr14:69445954-69447079	Hela-S3	cervix:	n/a	n/a
2	PML	chr14:69445698-69446550	MCF-7	breast:	n/a	n/a
3	CEBPD	chr14:69445812-69446318	HepG2	liver:	n/a	n/a
4	POLR2A	chr14:69444534-69446528	A549	lung:	n/a	n/a
5	REST	chr14:69445718-69446311	SK-N-SH	brain:	n/a	n/a
6	CREB1	chr14:69444340-69446611	HepG2	liver:	n/a	n/a
7	POLR2A	chr14:69443844-69447350	HUVEC	blood vessel:	n/a	n/a
8	TBP	chr14:69445806-69446332	HepG2	liver:	n/a	n/a
9	CREB1	chr14:69445805-69446553	H1-hESC	embryonic stem cell:	n/a	n/a
10	HDAC2	chr14:69445950-69446590	MCF-7	breast:	n/a	chr14:69446464-69446478
11	TAF1	chr14:69445756-69446495	H1-neurons	neurons:	n/a	n/a
12	TAF1	chr14:69445744-69446285	MCF-7	breast:	n/a	n/a
13	CEBPB	chr14:69445999-69446574	IMR90	lung:	n/a	n/a
14	CREB1	chr14:69445916-69446342	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr14:69445646-69446514	U87	brain:	n/a	n/a
16	MAX	chr14:69445663-69446573	ECC-1	luminal epithelium:	n/a	chr14:69446258-69446267 chr14:69446222-69446232 chr14:69446056-69446066 chr14:69446420-69446430
17	USF1	chr14:69446087-69446412	A549	lung:	n/a	chr14:69446257-69446268
18	EGR1	chr14:69445867-69446565	MCF-7	breast:	n/a	chr14:69446057-69446070 chr14:69446225-69446236 chr14:69446062-69446072 chr14:69446223-69446238 chr14:69446057-69446070 chr14:69446060-69446070 chr14:69446224-69446237 chr14:69446060-69446069 chr14:69446421-69446434 chr14:69446055-69446065 chr14:69446056-69446071 chr14:69446057-69446071 chr14:69446219-69446228 chr14:69446057-69446070 chr14:69446514-69446527 chr14:69446057-69446070
19	TAF1	chr14:69445650-69446554	ECC-1	luminal epithelium:	n/a	n/a
20	REST	chr14:69445812-69446117	SK-N-SH	brain:	n/a	n/a
21	HEY1	chr14:69445629-69446539	HepG2	liver:	n/a	chr14:69445945-69445960 chr14:69446057-69446072
22	ELF1	chr14:69444415-69446561	MCF-7	breast:	n/a	chr14:69446050-69446062 chr14:69446060-69446072 chr14:69445127-69445139 chr14:69445490-69445499
23	RCOR1	chr14:69445572-69446826	Hela-S3	cervix:	n/a	n/a
24	NFIC	chr14:69445711-69447088	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr14:69444423-69446910	K562	blood:	n/a	n/a
26	ATF2	chr14:69446047-69446417	H1-hESC	embryonic stem cell:	n/a	n/a
27	CEBPB	chr14:69445974-69446301	K562	blood:	n/a	n/a
28	POLR2A	chr14:69443926-69446789	ProgFib	skin:	n/a	n/a
29	SP1	chr14:69446037-69446262	GM12878	blood:	n/a	chr14:69446061-69446073 chr14:69446221-69446233 chr14:69446055-69446067 chr14:69446222-69446236 chr14:69446071-69446085 chr14:69446065-69446079 chr14:69446062-69446071 chr14:69446223-69446232 chr14:69446222-69446231 chr14:69446089-69446110 chr14:69446062-69446072 chr14:69446061-69446072 chr14:69446061-69446073 chr14:69446221-69446233 chr14:69446063-69446072 chr14:69446222-69446232
30	POLR2A	chr14:69444061-69446941	Hela-S3	cervix:	n/a	n/a
31	CEBPD	chr14:69445775-69446468	HepG2	liver:	n/a	n/a
32	CHD2	chr14:69444265-69447147	Hela-S3	cervix:	n/a	chr14:69446695-69446705
33	MXI1	chr14:69445771-69446478	HepG2	liver:	n/a	n/a
34	POLR2A	chr14:69445632-69446578	H1-neurons	neurons:	n/a	n/a
35	POLR2A	chr14:69441718-69446518	HepG2	liver:	n/a	n/a
36	POLR2A	chr14:69445635-69446486	SK-N-MC	brain:	n/a	n/a
37	CEBPB	chr14:69445821-69446453	HepG2	liver:	n/a	n/a
38	CREB1	chr14:69445787-69446485	A549	lung:	n/a	n/a
39	MYC	chr14:69446085-69446386	MCF10A-Er-Src	breast:	n/a	chr14:69446258-69446267 chr14:69446222-69446232
40	POLR2A	chr14:69444519-69446541	K562	blood:	n/a	n/a
41	MAX	chr14:69445627-69446512	K562	blood:	n/a	chr14:69446258-69446267 chr14:69446222-69446232 chr14:69446056-69446066 chr14:69445647-69445657 chr14:69446420-69446430
42	POLR2A	chr14:69445588-69446833	Hela-S3	cervix:	n/a	n/a
43	HDAC2	chr14:69445770-69446538	HepG2	liver:	n/a	chr14:69446464-69446478
44	MXI1	chr14:69441660-69447416	IMR90	lung:	n/a	n/a
45	MAX	chr14:69445832-69446400	HepG2	liver:	n/a	chr14:69446258-69446267 chr14:69446222-69446232 chr14:69446056-69446066
46	POLR2A	chr14:69444406-69446941	MCF-7	breast:	n/a	n/a
47	MAX	chr14:69443875-69446589	MCF-7	breast:	n/a	chr14:69446258-69446267 chr14:69446222-69446232 chr14:69444518-69444528 chr14:69445035-69445045 chr14:69445545-69445555 chr14:69446056-69446066 chr14:69445647-69445657 chr14:69446420-69446430
48	MAZ	chr14:69444590-69446975	K562	blood:	n/a	chr14:69446258-69446267 chr14:69446222-69446232 chr14:69445035-69445045 chr14:69445545-69445555 chr14:69446056-69446066 chr14:69445647-69445657 chr14:69446420-69446430
49	USF1	chr14:69446074-69446363	K562	blood:	n/a	chr14:69446257-69446268
50	USF1	chr14:69446074-69446406	A549	lung:	n/a	chr14:69446257-69446268

No.	Distal block	Cell Line	Cell type
1	chr14:69445082..69446680-chr19:821137..822637,2	MCF-7	breast:
2	chr14:69260551..69262457-chr14:69445515..69448155,2	MCF-7	breast:
3	chr14:69403117..69416483-chr14:69441657..69449888,50	MCF-7	breast:
4	chr1:110091081..110091606-chr14:69445610..69446367,2	Hela-S3	cervix:
5	chr14:69385888..69393669-chr14:69442988..69447287,14	MCF-7	breast:
6	chr14:69402982..69422523-chr14:69436263..69448017,46	MCF-7	breast:
7	chr14:69385676..69391979-chr14:69443116..69446617,6	MCF-7	breast:
8	chr12:46766203..46766769-chr14:69445809..69446525,2	Hela-S3	cervix:
9	chr14:69445219..69447444-chr3:183352751..183354827,2	MCF-7	breast:

Variant related genes	Relation type
ACTN1	TF binding region
ACTN1-AS1	TF binding region
ENSG00000114796	Chromatin interaction
ENSG00000072110	Chromatin interaction
ENSG00000258531	Chromatin interaction
ENSG00000065135	Chromatin interaction
ENSG00000185650	Chromatin interaction
ENSG00000129951	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10137547	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10139165	1.00[ASN][1000 genomes]
rs10147976	0.96[EUR][1000 genomes]
rs10220411	0.83[CEU][hapmap]
rs11620922	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11628549	1.00[ASN][1000 genomes]
rs17835996	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1884631	0.83[ASN][1000 genomes]
rs1950712	0.83[ASN][1000 genomes]
rs2012750	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2012764	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2012785	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2300875	0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2877521	0.83[ASN][1000 genomes]
rs2877522	0.83[ASN][1000 genomes]
rs2877523	0.83[ASN][1000 genomes]
rs60900044	1.00[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	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3449858	chr14:69443549-69447697	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv3409047	chr14:69444224-69447072	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3809393	ACTN1	Cis_1M	lymphoblastoid	RTeQTL
rs3809393	FNTB	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69443200-69447000	Active TSS	Aorta	Aorta
2	chr14:69443600-69446800	Active TSS	Esophagus	oesophagus
3	chr14:69443600-69447200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr14:69443800-69446800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr14:69443800-69446800	Active TSS	Right Atrium	heart
6	chr14:69443800-69446800	Active TSS	HSMM	muscle
7	chr14:69443800-69447200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr14:69443800-69447400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr14:69444000-69446800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr14:69444000-69446800	Active TSS	Brain Angular Gyrus	brain
11	chr14:69444000-69446800	Active TSS	Brain Substantia Nigra	brain
12	chr14:69444000-69447200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:69444000-69447200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr14:69444200-69446600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr14:69444200-69446800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr14:69444200-69446800	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr14:69444200-69446800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr14:69444200-69446800	Active TSS	Brain Anterior Caudate	brain
19	chr14:69444200-69446800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr14:69444200-69446800	Active TSS	Colon Smooth Muscle	Colon
21	chr14:69444200-69446800	Active TSS	Duodenum Mucosa	Duodenum
22	chr14:69444200-69446800	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr14:69444200-69446800	Active TSS	Fetal Intestine Large	intestine
24	chr14:69444200-69446800	Active TSS	Left Ventricle	heart
25	chr14:69444200-69446800	Active TSS	Pancreas	Pancrea
26	chr14:69444200-69446800	Active TSS	Placenta Amnion	Placenta Amnion
27	chr14:69444200-69446800	Active TSS	Psoas Muscle	Psoas
28	chr14:69444200-69446800	Active TSS	Rectal Smooth Muscle	rectum
29	chr14:69444200-69446800	Active TSS	Right Ventricle	heart
30	chr14:69444200-69446800	Active TSS	NHEK	skin
31	chr14:69444200-69446800	Active TSS	NHLF	lung
32	chr14:69444200-69447000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr14:69444200-69447000	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr14:69444200-69447000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr14:69444200-69447000	Active TSS	Fetal Kidney	kidney
36	chr14:69444200-69447000	Active TSS	Ovary	ovary
37	chr14:69444200-69447000	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr14:69444200-69447000	Active TSS	HSMMtube	muscle
39	chr14:69444200-69447200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr14:69444200-69447200	Active TSS	Brain Hippocampus Middle	brain
41	chr14:69444200-69447400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr14:69444400-69446200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr14:69444400-69446600	Active TSS	H1 Cell Line	embryonic stem cell
44	chr14:69444400-69446600	Active TSS	Primary monocytes fromperipheralblood	blood
45	chr14:69444400-69446600	Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr14:69444400-69446600	Active TSS	Primary T cells from cord blood	blood
47	chr14:69444400-69446600	Active TSS	Muscle Satellite Cultured Cells	--
48	chr14:69444400-69446600	Active TSS	Stomach Smooth Muscle	stomach
49	chr14:69444400-69446600	Active TSS	GM12878-XiMat	blood
50	chr14:69444400-69446600	Active TSS	NH-A	brain

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