Variant report

Variant	rs1488373
Chromosome Location	chr3:45957689-45957690
allele	C/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	YY1	chr3:45957105-45957774	GM12891	blood:	n/a	n/a
2	TCF12	chr3:45957074-45957774	GM12878	blood:	n/a	n/a
3	CEBPB	chr3:45955963-45958192	GM12878	blood:	n/a	n/a
4	BCL11A	chr3:45957066-45957767	GM12878	blood:	n/a	n/a
5	FOSL2	chr3:45957386-45957780	MCF-7	breast:	n/a	chr3:45957603-45957613 chr3:45957603-45957613 chr3:45957604-45957612 chr3:45957602-45957614 chr3:45957603-45957613 chr3:45957603-45957613
6	POLR2A	chr3:45957480-45957916	GM12891	blood:	n/a	n/a
7	EGR1	chr3:45957274-45957842	MCF-7	breast:	n/a	chr3:45957547-45957569
8	PAX5	chr3:45956907-45957924	GM12878	blood:	n/a	n/a
9	STAT3	chr3:45957571-45957752	MCF10A-Er-Src	breast:	n/a	chr3:45957656-45957668
10	CHD2	chr3:45956944-45957925	GM12878	blood:	n/a	chr3:45957264-45957274
11	EGR1	chr3:45957226-45957795	HCT-116	colon:	n/a	chr3:45957256-45957269 chr3:45957547-45957569
12	REST	chr3:45957111-45957705	GM12878	blood:	n/a	n/a
13	STAT1	chr3:45957248-45957751	GM12878	blood:	n/a	chr3:45957656-45957668 chr3:45957262-45957274
14	FOS	chr3:45957455-45957776	MCF10A-Er-Src	breast:	n/a	chr3:45957603-45957613 chr3:45957603-45957613 chr3:45957604-45957612 chr3:45957602-45957614 chr3:45957603-45957613 chr3:45957603-45957613
15	POLR2A	chr3:45956385-45958145	GM12878	blood:	n/a	n/a
16	MYC	chr3:45957535-45957744	MCF10A-Er-Src	breast:	n/a	n/a
17	GATA3	chr3:45957426-45957789	MCF-7	breast:	n/a	n/a
18	NRF1	chr3:45957152-45957774	GM12878	blood:	n/a	n/a
19	NFATC1	chr3:45956986-45957788	GM12878	blood:	n/a	n/a
20	BATF	chr3:45957111-45957763	GM12878	blood:	n/a	n/a
21	CHD1	chr3:45956868-45957772	GM12878	blood:	n/a	chr3:45957264-45957274
22	FOS	chr3:45957477-45957772	MCF10A-Er-Src	breast:	n/a	chr3:45957603-45957613 chr3:45957603-45957613 chr3:45957604-45957612 chr3:45957602-45957614 chr3:45957603-45957613 chr3:45957603-45957613
23	E2F4	chr3:45957550-45957776	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr3:45957383-45957772	GM12892	blood:	n/a	n/a
25	EGR1	chr3:45957226-45957853	MCF-7	breast:	n/a	chr3:45957256-45957269 chr3:45957547-45957569
26	BCL3	chr3:45956271-45957917	GM12878	blood:	n/a	chr3:45956839-45956848
27	TAF1	chr3:45957033-45957785	GM12878	blood:	n/a	n/a
28	MXI1	chr3:45956917-45957786	GM12878	blood:	n/a	n/a
29	NFIC	chr3:45956857-45957971	GM12878	blood:	n/a	n/a
30	EGR1	chr3:45957390-45957718	GM12878	blood:	n/a	chr3:45957547-45957569
31	STAT5A	chr3:45956257-45958291	GM12878	blood:	n/a	chr3:45957656-45957668 chr3:45957262-45957274 chr3:45956840-45956852
32	ZNF384	chr3:45957053-45957696	GM12878	blood:	n/a	n/a
33	POU2F2	chr3:45957050-45957767	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:45957594-45957863	GM12891	blood:	n/a	n/a
35	EP300	chr3:45957139-45957703	GM12878	blood:	n/a	chr3:45957513-45957523
36	FOS	chr3:45957475-45957742	MCF10A-Er-Src	breast:	n/a	chr3:45957603-45957613 chr3:45957603-45957613 chr3:45957602-45957614 chr3:45957603-45957613 chr3:45957603-45957613 chr3:45957604-45957612
37	RELA	chr3:45957131-45957897	GM15510	blood:	n/a	n/a
38	EP300	chr3:45957137-45957776	GM12878	blood:	n/a	chr3:45957513-45957523
39	FOXM1	chr3:45956890-45958175	GM12878	blood:	n/a	n/a
40	HDAC2	chr3:45957312-45957734	MCF-7	breast:	n/a	chr3:45957513-45957522
41	RELA	chr3:45957051-45957854	GM19099	blood:	n/a	n/a
42	POU2F2	chr3:45956959-45957824	GM12878	blood:	n/a	n/a
43	SIN3A	chr3:45957088-45957810	GM12878	blood:	n/a	n/a
44	ZNF217	chr3:45957344-45957697	MCF-7	breast:	n/a	n/a
45	POLR2A	chr3:45955919-45957825	GM12878	blood:	n/a	n/a
46	SP1	chr3:45957006-45957829	GM12878	blood:	n/a	chr3:45957659-45957669 chr3:45957660-45957669 chr3:45957659-45957668 chr3:45957660-45957669 chr3:45957659-45957669 chr3:45957658-45957670 chr3:45957658-45957670 chr3:45957260-45957272 chr3:45957655-45957669 chr3:45957261-45957270 chr3:45957264-45957278 chr3:45957257-45957271
47	RELA	chr3:45957140-45957794	GM12878	blood:	n/a	n/a
48	EBF1	chr3:45957024-45957877	GM12878	blood:	n/a	n/a
49	RELA	chr3:45957084-45957852	GM18505	blood:	n/a	n/a
50	CUX1	chr3:45956965-45957864	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:45957664-45957714	ProgFib	skin:	n/a
2	chr3:45957664-45957714	BJ	skin:	n/a
3	chr3:45957664-45957714	GM06990	blood:	n/a
4	chr3:45957664-45957714	HCF	heart:	n/a
5	chr3:45957664-45957714	T-47D	breast:	n/a
6	chr3:45957664-45957714	AG09309	skin:	n/a
7	chr3:45957664-45957714	HCPEpiC	choroid plexus:	n/a
8	chr3:45957664-45957714	PrEC	prostate:	n/a
9	chr3:45957664-45957714	HPAEpiC	pulmonary alveolar:	n/a
10	chr3:45957664-45957714	HCM	heart:	n/a
11	chr3:45957664-45957714	NB4	blood:	n/a
12	chr3:45957664-45957714	AG04450	lung:	fetal
13	chr3:45957664-45957714	HEK293	kidney:	embryo
14	chr3:45957664-45957714	ECC-1	luminal epithelium:	n/a
15	chr3:45957664-45957714	HRPEpiC	eye:	n/a
16	chr3:45957664-45957714	HMEC	breast:	n/a
17	chr3:45957664-45957714	HepG2	liver:	n/a
18	chr3:45957664-45957714	HRCEpiC	kidney:	n/a
19	chr3:45957664-45957714	SAEC	small airway:	n/a
20	chr3:45957664-45957714	IMR90	lung:	fetal
21	chr3:45957664-45957714	PANC-1	pancreas:	n/a
22	chr3:45957664-45957714	SKMC	muscle:	n/a
23	chr3:45957664-45957714	HIPEpiC	eye:	n/a
24	chr3:45957664-45957714	NHDF-neo	bronchial:	n/a
25	chr3:45957664-45957714	SK-N-SH	brain:	n/a
26	chr3:45957664-45957714	HRE	kidney:	n/a
27	chr3:45957664-45957714	GM12892	blood:	n/a
28	chr3:45957664-45957714	BE2_C	brain:	n/a
29	chr3:45957664-45957714	HNPCEpiC	eye:	n/a
30	chr3:45957664-45957714	HL-60	blood:	n/a
31	chr3:45957664-45957714	NH-A	brain:	n/a
32	chr3:45957664-45957714	AG10803	skin:	n/a
33	chr3:45957664-45957714	SK-N-MC	brain:	n/a
34	chr3:45957664-45957714	NHBE	bronchial:	n/a
35	chr3:45957664-45957714	Jurkat	blood:	n/a
36	chr3:45957664-45957714	MCF-7	breast:	n/a
37	chr3:45957664-45957714	ovcar-3	ovarian:	n/a
38	chr3:45957664-45957714	AG04449	skin:	fetal
39	chr3:45957664-45957714	K562	blood:	n/a
40	chr3:45957664-45957714	H1-hESC	embryonic stem cell:	embryo
41	chr3:45957664-45957714	CMK	blood:	n/a
42	chr3:45957664-45957714	MCF10A-Er-Src	breast:	n/a
43	chr3:45957664-45957714	AoSMC	blood vessel:	n/a
44	chr3:45957664-45957714	Hepatocyte	liver:	n/a
45	chr3:45957664-45957714	GM19239	blood:	n/a
46	chr3:45957664-45957714	GM12891	blood:	n/a
47	chr3:45957664-45957714	HCT-116	colon:	n/a
48	chr3:45957664-45957714	PFSK-1	brain:	n/a
49	chr3:45957664-45957714	HEEpiC	esophagus:	n/a
50	chr3:45957664-45957714	A549	lung:	n/a

Variant related genes	Relation type
LZTFL1	TF binding region
LZTFL1	CpG island

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1047444	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1488374	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1532070	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2191030	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2373088	0.81[EUR][1000 genomes]
rs4682801	0.94[GIH][hapmap]
rs6441934	1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs6764244	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6802312	0.94[GIH][hapmap]
rs6806802	0.82[EUR][1000 genomes]
rs7130	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7618618	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7634640	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7652331	0.90[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9311379	0.84[EUR][1000 genomes]
rs9810934	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1488373	FYCO1	cis	lung	GTEx
rs1488373	FYCO1	cis	Nerve Tibial	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45932400-45960200	Weak transcription	Fetal Intestine Small	intestine
2	chr3:45934000-45960200	Weak transcription	Right Ventricle	heart
3	chr3:45940000-45959800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:45941400-45960000	Weak transcription	Adipose Nuclei	Adipose
5	chr3:45943000-45961000	Weak transcription	Brain Substantia Nigra	brain
6	chr3:45943600-45961200	Weak transcription	Gastric	stomach
7	chr3:45946200-45960400	Weak transcription	Aorta	Aorta
8	chr3:45947000-45960200	Weak transcription	Lung	lung
9	chr3:45948200-45961000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:45948400-45961600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:45948800-45960200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:45949200-45962400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:45949400-45958400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:45949800-45962600	Weak transcription	HepG2	liver
15	chr3:45950000-45960800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:45950200-45959800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:45950200-45960000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:45950200-45960400	Weak transcription	Pancreas	Pancrea
19	chr3:45950400-45958800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:45950800-45958800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:45952800-45963600	Weak transcription	Psoas Muscle	Psoas
22	chr3:45952800-45964600	Weak transcription	Fetal Heart	heart
23	chr3:45953200-45959200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:45953200-45959600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:45953200-45960800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:45953400-45959800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:45955200-45958400	Flanking Active TSS	Fetal Thymus	thymus
28	chr3:45955800-45960000	Weak transcription	Fetal Intestine Large	intestine
29	chr3:45956200-45957800	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr3:45956200-45958200	Enhancers	Primary B cells from cord blood	blood
31	chr3:45956200-45958200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:45956200-45958600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:45956200-45958600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:45956200-45959400	Flanking Active TSS	Thymus	Thymus
35	chr3:45956400-45957800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:45956400-45958000	Enhancers	HSMM	muscle
37	chr3:45956400-45958200	Enhancers	Primary B cells from peripheral blood	blood
38	chr3:45956400-45959600	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:45956600-45957800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:45956600-45957800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr3:45956600-45957800	Weak transcription	Spleen	Spleen
42	chr3:45956600-45958800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:45956600-45960200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr3:45956800-45957800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
45	chr3:45956800-45957800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr3:45956800-45957800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:45956800-45958000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:45956800-45958000	Enhancers	NH-A	brain
49	chr3:45956800-45958400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:45956800-45958600	Enhancers	Small Intestine	intestine

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