Variant report

Variant	rs55970459
Chromosome Location	chr5:58336193-58336194
allele	C/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	FOXA2	chr5:58336190-58336747	A549	lung:	n/a	n/a
2	TEAD4	chr5:58335378-58336513	A549	lung:	n/a	n/a
3	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
4	POLR2A	chr5:58334257-58336743	PFSK-1	brain:	n/a	n/a
5	MAX	chr5:58335050-58336938	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
6	POLR2A	chr5:58336055-58336313	A549	lung:	n/a	n/a
7	MYC	chr5:58336006-58336681	MCF10A-Er-Src	breast:	n/a	chr5:58336206-58336221 chr5:58336206-58336216
8	NR3C1	chr5:58336123-58336470	A549	lung:	n/a	chr5:58336384-58336401
9	FOXA2	chr5:58336042-58336612	A549	lung:	n/a	chr5:58336091-58336103 chr5:58336082-58336094
10	REST	chr5:58335991-58336481	HL-60	blood:	n/a	n/a
11	SIN3AK20	chr5:58335945-58336572	A549	lung:	n/a	n/a
12	STAT3	chr5:58336073-58336373	MCF10A-Er-Src	breast:	n/a	n/a
13	MAX	chr5:58334405-58337505	NB4	blood:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
14	FOS	chr5:58336090-58336377	MCF10A-Er-Src	breast:	n/a	n/a
15	NR3C1	chr5:58335994-58336529	A549	lung:	n/a	chr5:58336384-58336401
16	MYC	chr5:58333863-58336853	NB4	blood:	n/a	chr5:58336786-58336799 chr5:58336783-58336802 chr5:58336788-58336798 chr5:58336206-58336221 chr5:58336788-58336797 chr5:58336206-58336216 chr5:58336787-58336798 chr5:58336788-58336798 chr5:58336787-58336798 chr5:58336791-58336799
17	POLR2A	chr5:58335999-58336520	HL-60	blood:	n/a	n/a
18	REST	chr5:58336056-58336587	A549	lung:	n/a	n/a
19	MAX	chr5:58334729-58337074	HepG2	liver:	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
20	GATA3	chr5:58334373-58336526	A549	lung:	n/a	n/a
21	NFIC	chr5:58336159-58337097	HepG2	liver:	n/a	n/a
22	POLR2A	chr5:58334860-58336670	PFSK-1	brain:	n/a	n/a
23	NR2F2	chr5:58336095-58337111	HepG2	liver:	n/a	n/a
24	POLR2A	chr5:58333046-58336833	A549	lung:	n/a	n/a
25	SIX5	chr5:58330273-58336780	A549	lung:	n/a	chr5:58334021-58334030
26	BCL3	chr5:58335000-58338690	A549	lung:	n/a	chr5:58335393-58335406 chr5:58336423-58336432 chr5:58335440-58335453
27	POLR2A	chr5:58336151-58336390	HepG2	liver:	n/a	n/a
28	RCOR1	chr5:58335409-58336522	HepG2	liver:	n/a	n/a
29	REST	chr5:58331372-58337614	A549	lung:	n/a	chr5:58334044-58334052 chr5:58335557-58335570
30	FOXA1	chr5:58336192-58337025	HepG2	liver:	n/a	chr5:58336895-58336910
31	MXI1	chr5:58334271-58336440	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr5:58336005-58336600	Hela-S3	cervix:	n/a	n/a
33	MXI1	chr5:58334805-58336915	HepG2	liver:	n/a	chr5:58336789-58336798
34	NR3C1	chr5:58336019-58336615	A549	lung:	n/a	chr5:58336384-58336401
35	POLR2A	chr5:58336186-58336303	A549	lung:	n/a	n/a
36	SP1	chr5:58331577-58338881	A549	lung:	n/a	chr5:58333512-58333519 chr5:58335988-58335997
37	SIN3AK20	chr5:58335870-58336892	A549	lung:	n/a	n/a
38	EP300	chr5:58334760-58337676	A549	lung:	n/a	chr5:58336263-58336277
39	POLR2A	chr5:58331579-58336345	IMR90	lung:	n/a	n/a
40	STAT3	chr5:58336084-58336360	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr5:58336042-58336382	MCF10A-Er-Src	breast:	n/a	n/a
42	JUND	chr5:58335821-58336633	A549	lung:	n/a	n/a
43	POLR2A	chr5:58334182-58336389	A549	lung:	n/a	n/a
44	FOS	chr5:58336006-58336413	MCF10A-Er-Src	breast:	n/a	n/a
45	NR3C1	chr5:58335976-58336577	A549	lung:	n/a	chr5:58336384-58336401
46	CEBPB	chr5:58335998-58336546	A549	lung:	n/a	chr5:58336259-58336276 chr5:58336262-58336275
47	TAF1	chr5:58332948-58336675	A549	lung:	n/a	n/a
48	MBD4	chr5:58336103-58336992	HepG2	liver:	n/a	n/a
49	MAX	chr5:58336063-58336239	HepG2	liver:	n/a	chr5:58336206-58336221 chr5:58336206-58336216
50	SMC3	chr5:58336089-58336420	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:65588255..65588778-chr5:58336015..58336662,2	NB4	blood:
2	chr5:58329365..58331017-chr5:58335790..58337572,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB3C-1	chr5:58335035-58336614	NONHSAT101625

Variant related genes	Relation type
PDE4D	TF binding region
ENSG00000199568	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10514871	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498602	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1498607	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498609	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17720311	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17776777	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17776825	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279737	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55946132	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56057207	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62358506	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72770683	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][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

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58330400-58336400	Active TSS	Right Ventricle	heart
2	chr5:58330400-58336600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:58330600-58336200	Active TSS	Right Atrium	heart
4	chr5:58331000-58336200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:58331000-58336400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:58331000-58336600	Active TSS	Psoas Muscle	Psoas
7	chr5:58333000-58336200	Active TSS	Left Ventricle	heart
8	chr5:58333400-58336200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:58333600-58336400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr5:58334200-58336200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:58334200-58336200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:58334200-58336200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr5:58334400-58336200	Active TSS	Aorta	Aorta
14	chr5:58334600-58336200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
15	chr5:58334600-58336200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr5:58334800-58336200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr5:58334800-58336200	Active TSS	Brain Angular Gyrus	brain
18	chr5:58334800-58336200	Active TSS	Rectal Smooth Muscle	rectum
19	chr5:58334800-58336200	Active TSS	Stomach Mucosa	stomach
20	chr5:58334800-58336400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr5:58334800-58336400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:58334800-58336400	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr5:58335000-58336200	Active TSS	Brain Hippocampus Middle	brain
24	chr5:58335000-58336200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:58335000-58336200	Active TSS	Colonic Mucosa	Colon
26	chr5:58335000-58336200	Active TSS	Fetal Muscle Trunk	muscle
27	chr5:58335000-58336200	Active TSS	Pancreas	Pancrea
28	chr5:58335000-58336200	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr5:58335000-58336400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
30	chr5:58335000-58336400	Active TSS	Duodenum Mucosa	Duodenum
31	chr5:58335000-58336400	Active TSS	A549	lung
32	chr5:58335000-58336600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:58335000-58336600	Bivalent Enhancer	Fetal Brain Male	brain
34	chr5:58335400-58336200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:58335400-58336400	Bivalent/Poised TSS	NHEK	skin
36	chr5:58335600-58336200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:58335600-58336200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr5:58335600-58336200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:58335600-58336200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr5:58335600-58336400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr5:58335600-58336600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr5:58335600-58336600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
43	chr5:58335800-58336200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:58335800-58336200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:58335800-58336200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:58335800-58336200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr5:58335800-58336200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr5:58335800-58336200	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr5:58335800-58336200	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr5:58335800-58336200	Flanking Active TSS	Placenta	Placenta

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