Variant report

Variant	rs1007407
Chromosome Location	chr14:69446960-69446961
allele	A/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	CEBPB	chr14:69445954-69447079	Hela-S3	cervix:	n/a	n/a
2	MAX	chr14:69446717-69447230	NB4	blood:	n/a	n/a
3	POLR2A	chr14:69443844-69447350	HUVEC	blood vessel:	n/a	n/a
4	E2F6	chr14:69446596-69447567	H1-hESC	embryonic stem cell:	n/a	chr14:69446689-69446701 chr14:69447064-69447076
5	NFIC	chr14:69445711-69447088	ECC-1	luminal epithelium:	n/a	n/a
6	CHD2	chr14:69444265-69447147	Hela-S3	cervix:	n/a	chr14:69446695-69446705
7	MXI1	chr14:69441660-69447416	IMR90	lung:	n/a	n/a
8	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
9	CHD1	chr14:69441180-69450261	IMR90	lung:	n/a	chr14:69446695-69446705
10	SMC3	chr14:69445809-69447168	Hela-S3	cervix:	n/a	chr14:69446348-69446358
11	ZNF143	chr14:69446735-69447205	H1-hESC	embryonic stem cell:	n/a	n/a
12	NR2F2	chr14:69445625-69447238	MCF-7	breast:	n/a	n/a
13	MAX	chr14:69446593-69447414	MCF-7	breast:	n/a	n/a
14	SIN3A	chr14:69444455-69447300	H1-hESC	embryonic stem cell:	n/a	chr14:69444765-69444778 chr14:69444777-69444790 chr14:69445945-69445958 chr14:69445831-69445844
15	EP300	chr14:69444197-69447183	ECC-1	luminal epithelium:	n/a	chr14:69445444-69445460 chr14:69444809-69444825 chr14:69446463-69446477 chr14:69445133-69445142 chr14:69445465-69445481 chr14:69445645-69445661 chr14:69446770-69446786
16	RAD21	chr14:69446515-69447242	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr14:69444097-69447251	Hela-S3	cervix:	n/a	n/a
18	NANOG	chr14:69446661-69447073	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr14:69446593-69447388	H1-hESC	embryonic stem cell:	n/a	n/a
20	STAT3	chr14:69446819-69447019	MCF10A-Er-Src	breast:	n/a	n/a
21	MAZ	chr14:69442284-69447004	IMR90	lung:	n/a	chr14:69442450-69442457 chr14:69442448-69442459 chr14:69446258-69446267 chr14:69446222-69446232 chr14:69442447-69442460 chr14:69444518-69444528 chr14:69445035-69445045 chr14:69442449-69442459 chr14:69445545-69445555 chr14:69446056-69446066 chr14:69445647-69445657 chr14:69446420-69446430 chr14:69442449-69442458
22	E2F4	chr14:69446640-69447263	Hela-S3	cervix:	n/a	chr14:69446689-69446701 chr14:69447064-69447076
23	MYC	chr14:69446916-69447185	MCF10A-Er-Src	breast:	n/a	n/a
24	E2F4	chr14:69445936-69447288	MCF10A-Er-Src	breast:	n/a	chr14:69446056-69446065 chr14:69446372-69446384 chr14:69446689-69446701 chr14:69446062-69446071 chr14:69447064-69447076 chr14:69445954-69445964
25	NFIC	chr14:69445811-69447091	ECC-1	luminal epithelium:	n/a	n/a
26	MAX	chr14:69444349-69447398	ECC-1	luminal epithelium:	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
27	MAX	chr14:69446598-69447457	ECC-1	luminal epithelium:	n/a	n/a
28	MYC	chr14:69446887-69447129	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr14:69446847-69447047	HepG2	liver:	n/a	n/a
30	MAX	chr14:69444376-69447340	A549	lung:	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
31	NFYA	chr14:69446643-69447106	Hela-S3	cervix:	n/a	n/a
32	TCF12	chr14:69445655-69447074	A549	lung:	n/a	chr14:69446152-69446160 chr14:69445831-69445841
33	HDAC2	chr14:69445835-69447112	H1-hESC	embryonic stem cell:	n/a	chr14:69446464-69446478
34	ATF2	chr14:69446597-69447196	H1-hESC	embryonic stem cell:	n/a	n/a
35	RFX5	chr14:69446661-69447058	Hela-S3	cervix:	n/a	n/a
36	MAX	chr14:69446601-69447367	MCF-7	breast:	n/a	n/a
37	POLR2A	chr14:69443929-69446974	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr14:69446573-69447056	ECC-1	luminal epithelium:	n/a	n/a
39	MYC	chr14:69444576-69446985	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
40	TAF1	chr14:69446946-69447237	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr14:69446867-69447132	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr14:69444325-69447439	A549	lung:	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
43	MAX	chr14:69446756-69447366	HepG2	liver:	n/a	n/a
44	MAX	chr14:69446854-69447342	H1-hESC	embryonic stem cell:	n/a	n/a
45	E2F6	chr14:69446578-69447421	H1-hESC	embryonic stem cell:	n/a	chr14:69446689-69446701 chr14:69447064-69447076
46	TEAD4	chr14:69445684-69447234	ECC-1	luminal epithelium:	n/a	n/a
47	TEAD4	chr14:69445773-69447283	ECC-1	luminal epithelium:	n/a	n/a
48	HCFC1	chr14:69443969-69447466	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr14:69446881-69447141	SK-N-SH	brain:	n/a	n/a
50	MXI1	chr14:69442097-69447256	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:69260551..69262457-chr14:69445515..69448155,2	MCF-7	breast:
2	chr14:69403117..69416483-chr14:69441657..69449888,50	MCF-7	breast:
3	chr14:69385888..69393669-chr14:69442988..69447287,14	MCF-7	breast:
4	chr14:69402982..69422523-chr14:69436263..69448017,46	MCF-7	breast:
5	chr14:69445219..69447444-chr3:183352751..183354827,2	MCF-7	breast:

Variant related genes	Relation type
ACTN1	TF binding region
ENSG00000114796	Chromatin interaction
ENSG00000185650	Chromatin interaction
ENSG00000072110	Chromatin interaction
ENSG00000258531	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10083451	0.82[JPT][hapmap]
rs10130013	1.00[JPT][hapmap]
rs10137547	0.96[ASN][1000 genomes]
rs10139873	0.82[JPT][hapmap]
rs10143302	1.00[JPT][hapmap]
rs10145565	0.82[JPT][hapmap]
rs10146339	1.00[JPT][hapmap]
rs10147369	1.00[JPT][hapmap]
rs10147976	0.96[ASN][1000 genomes]
rs10149232	1.00[JPT][hapmap]
rs11158782	0.82[JPT][hapmap]
rs11158787	1.00[JPT][hapmap]
rs11158790	0.82[JPT][hapmap]
rs1147481	0.82[JPT][hapmap]
rs11622889	1.00[JPT][hapmap]
rs11628126	1.00[JPT][hapmap]
rs12431846	1.00[JPT][hapmap]
rs12432970	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12434478	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs12434775	1.00[JPT][hapmap]
rs12435594	1.00[JPT][hapmap]
rs12589028	0.82[JPT][hapmap]
rs1275407	0.82[JPT][hapmap]
rs1275415	1.00[JPT][hapmap]
rs17093668	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17106670	0.87[ASN][1000 genomes]
rs1892297	1.00[JPT][hapmap]
rs1914004	1.00[JPT][hapmap]
rs2001998	0.82[JPT][hapmap]
rs2012750	0.96[ASN][1000 genomes]
rs2012764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2012785	0.96[ASN][1000 genomes]
rs2024892	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2024893	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2056153	1.00[JPT][hapmap]
rs2268968	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2300875	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28561965	0.96[ASN][1000 genomes]
rs28613298	0.82[JPT][hapmap]
rs4243632	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902682	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs6573869	0.82[JPT][hapmap]
rs7140680	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7140693	0.88[CHD][hapmap]
rs7149487	0.87[ASN][1000 genomes]
rs7160629	0.82[JPT][hapmap]
rs72733548	0.83[ASN][1000 genomes]
rs8008184	1.00[JPT][hapmap]
rs8016537	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9323524	0.82[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1007407	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	chr14:69443600-69447200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr14:69443800-69447200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr14:69443800-69447400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:69444000-69447200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:69444000-69447200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr14:69444200-69447000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:69444200-69447000	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr14:69444200-69447000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr14:69444200-69447000	Active TSS	Fetal Kidney	kidney
11	chr14:69444200-69447000	Active TSS	Ovary	ovary
12	chr14:69444200-69447000	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr14:69444200-69447000	Active TSS	HSMMtube	muscle
14	chr14:69444200-69447200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr14:69444200-69447200	Active TSS	Brain Hippocampus Middle	brain
16	chr14:69444200-69447400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr14:69444400-69447000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr14:69444400-69447000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr14:69444400-69447000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr14:69444400-69447000	Active TSS	HMEC	breast
21	chr14:69444400-69447200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:69444400-69447200	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr14:69444400-69447200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr14:69444400-69447200	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr14:69444400-69447200	Active TSS	Fetal Brain Female	brain
26	chr14:69444400-69447400	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr14:69444600-69447000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr14:69444600-69447200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr14:69444600-69447400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:69445400-69447000	Bivalent/Poised TSS	Thymus	Thymus
31	chr14:69446000-69447000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
32	chr14:69446200-69447000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
33	chr14:69446200-69447000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
34	chr14:69446200-69447000	Flanking Active TSS	Placenta	Placenta
35	chr14:69446200-69447000	Flanking Bivalent TSS/Enh	Dnd41	blood
36	chr14:69446200-69447200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr14:69446200-69447200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr14:69446600-69447000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr14:69446600-69447000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr14:69446600-69447000	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr14:69446600-69447000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr14:69446600-69447000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr14:69446600-69447000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr14:69446600-69447000	Flanking Active TSS	Colonic Mucosa	Colon
45	chr14:69446600-69447000	Bivalent/Poised TSS	GM12878-XiMat	blood
46	chr14:69446600-69447200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr14:69446600-69447200	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr14:69446600-69447200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr14:69446600-69447200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr14:69446600-69447200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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