Variant report

Variant	rs4700319
Chromosome Location	chr5:58333808-58333809
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	CEBPB	chr5:58333788-58333939	Hela-S3	cervix:	n/a	n/a
2	MYC	chr5:58333738-58337715	A549	lung:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337561-58337571 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
3	BRCA1	chr5:58333455-58333866	Hela-S3	cervix:	n/a	n/a
4	ATF3	chr5:58333802-58335020	A549	lung:	n/a	n/a
5	STAT3	chr5:58333488-58334045	MCF10A-Er-Src	breast:	n/a	n/a
6	SIN3AK20	chr5:58333591-58334792	A549	lung:	n/a	n/a
7	FOSL2	chr5:58333394-58334913	A549	lung:	n/a	n/a
8	POLR2A	chr5:58333046-58336833	A549	lung:	n/a	n/a
9	SIX5	chr5:58330273-58336780	A549	lung:	n/a	chr5:58334021-58334030
10	REST	chr5:58331372-58337614	A549	lung:	n/a	chr5:58334044-58334052 chr5:58335557-58335570
11	POLR2A	chr5:58333767-58333829	A549	lung:	n/a	n/a
12	FOS	chr5:58333584-58334005	MCF10A-Er-Src	breast:	n/a	n/a
13	SP1	chr5:58331577-58338881	A549	lung:	n/a	chr5:58333512-58333519 chr5:58335988-58335997
14	FOS	chr5:58333621-58333927	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr5:58331579-58336345	IMR90	lung:	n/a	n/a
16	TAF1	chr5:58332948-58336675	A549	lung:	n/a	n/a
17	POLR2A	chr5:58332062-58336640	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr5:58331492-58333960	PFSK-1	brain:	n/a	n/a
19	BCL3	chr5:58333566-58336736	A549	lung:	n/a	chr5:58335393-58335406 chr5:58336423-58336432 chr5:58335440-58335453
20	BCL3	chr5:58330017-58334935	A549	lung:	n/a	chr5:58332249-58332258 chr5:58333393-58333401
21	ETS1	chr5:58333646-58335639	A549	lung:	n/a	chr5:58334179-58334195
22	POLR2A	chr5:58333710-58334821	PFSK-1	brain:	n/a	n/a
23	YY1	chr5:58333728-58334136	A549	lung:	n/a	n/a
24	MAX	chr5:58333387-58337168	A549	lung:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
25	CEBPB	chr5:58333354-58337052	A549	lung:	n/a	chr5:58336259-58336276 chr5:58334048-58334060 chr5:58336262-58336275
26	EP300	chr5:58333045-58334746	A549	lung:	n/a	chr5:58333921-58333930
27	EP300	chr5:58333033-58335096	A549	lung:	n/a	chr5:58333921-58333930
28	REST	chr5:58333746-58335724	A549	lung:	n/a	chr5:58334044-58334052 chr5:58335557-58335570
29	POLR2A	chr5:58333751-58333873	A549	lung:	n/a	n/a
30	SIN3AK20	chr5:58332967-58335742	A549	lung:	n/a	n/a
31	GATA3	chr5:58330035-58338800	A549	lung:	n/a	chr5:58333570-58333591 chr5:58332852-58332859 chr5:58333577-58333587 chr5:58333577-58333584 chr5:58332250-58332259 chr5:58333577-58333584 chr5:58332852-58332859 chr5:58333577-58333584 chr5:58333572-58333588 chr5:58336798-58336814 chr5:58332852-58332859
32	MAX	chr5:58333100-58339130	A549	lung:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337561-58337571 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
33	POLR2A	chr5:58333771-58333954	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr5:58331748-58336528	MCF10A-Er-Src	breast:	n/a	n/a
35	SP1	chr5:58332949-58337033	A549	lung:	n/a	chr5:58333512-58333519 chr5:58335988-58335997
36	TCF12	chr5:58331291-58337478	A549	lung:	n/a	chr5:58336418-58336428 chr5:58336399-58336408
37	CHD1	chr5:58331417-58336301	IMR90	lung:	n/a	n/a
38	POLR2A	chr5:58333694-58334130	Hela-S3	cervix:	n/a	n/a
39	STAT3	chr5:58333807-58333992	MCF10A-Er-Src	breast:	n/a	n/a
40	MYC	chr5:58333615-58334259	MCF10A-Er-Src	breast:	n/a	n/a
41	MXI1	chr5:58331564-58334104	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000247345	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1006431	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11738454	0.86[EUR][1000 genomes]
rs13181587	0.88[EUR][1000 genomes]
rs1498604	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498605	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498606	0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16889129	0.81[CEU][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs4699934	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450500	0.86[AMR][1000 genomes];0.94[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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4700319	DDX4	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58320200-58334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:58321800-58334000	Weak transcription	Gastric	stomach
3	chr5:58327000-58334000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:58330400-58336400	Active TSS	Right Ventricle	heart
5	chr5:58330400-58336600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:58330600-58334600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:58330600-58335000	Transcr. at gene 5' and 3'	A549	lung
8	chr5:58330600-58336200	Active TSS	Right Atrium	heart
9	chr5:58330800-58335800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr5:58331000-58336200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:58331000-58336400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:58331000-58336600	Active TSS	Psoas Muscle	Psoas
13	chr5:58331200-58334400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:58331600-58334200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr5:58332000-58334400	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr5:58332000-58334800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr5:58332000-58335200	Active TSS	Placenta Amnion	Placenta Amnion
18	chr5:58332000-58335800	Active TSS	HSMM	muscle
19	chr5:58332400-58334200	Active TSS	Primary T cells fromperipheralblood	blood
20	chr5:58332400-58335000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:58332600-58334000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr5:58332600-58334000	Active TSS	Fetal Muscle Leg	muscle
23	chr5:58332600-58334400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:58332800-58334200	Weak transcription	Fetal Intestine Large	intestine
25	chr5:58332800-58334400	Weak transcription	HMEC	breast
26	chr5:58332800-58334800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:58333000-58334000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr5:58333000-58334000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:58333000-58334200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:58333000-58334400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:58333000-58334400	Active TSS	Fetal Muscle Trunk	muscle
32	chr5:58333000-58334400	Flanking Active TSS	Osteobl	bone
33	chr5:58333000-58334800	Flanking Active TSS	NHEK	skin
34	chr5:58333000-58335000	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr5:58333000-58335800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:58333000-58336200	Active TSS	Left Ventricle	heart
37	chr5:58333200-58334000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:58333200-58334200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:58333200-58334200	Active TSS	Fetal Stomach	stomach
40	chr5:58333200-58334400	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr5:58333200-58334600	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr5:58333200-58336000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr5:58333400-58334000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:58333400-58334000	Active TSS	Placenta	Placenta
45	chr5:58333400-58334200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:58333400-58334200	Active TSS	Fetal Brain Male	brain
47	chr5:58333400-58334400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:58333400-58334400	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr5:58333400-58334400	Flanking Active TSS	Thymus	Thymus
50	chr5:58333400-58334600	Flanking Active TSS	Fetal Heart	heart

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