Variant report

Variant	rs17013486
Chromosome Location	chr4:129495243-129495244
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	BCL3	chr4:129494759-129495427	A549	lung:	n/a	n/a
2	TEAD4	chr4:129494835-129495372	HepG2	liver:	n/a	n/a
3	GABPA	chr4:129494935-129495308	A549	lung:	n/a	n/a
4	NR3C1	chr4:129494845-129495378	A549	lung:	n/a	chr4:129495200-129495226
5	TCF12	chr4:129494741-129495507	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr4:129494839-129495480	A549	lung:	n/a	n/a
7	TEAD4	chr4:129494793-129495425	SK-N-SH	brain:	n/a	n/a
8	NR3C1	chr4:129495079-129495264	A549	lung:	n/a	chr4:129495200-129495226
9	MAX	chr4:129494775-129495490	A549	lung:	n/a	n/a
10	TCF12	chr4:129494530-129496335	A549	lung:	n/a	n/a
11	NR3C1	chr4:129494749-129495502	A549	lung:	n/a	chr4:129495200-129495226
12	SIN3AK20	chr4:129494983-129495418	A549	lung:	n/a	n/a
13	TEAD4	chr4:129494801-129495560	A549	lung:	n/a	n/a
14	ELF1	chr4:129494917-129495388	A549	lung:	n/a	n/a
15	JUND	chr4:129494910-129495290	A549	lung:	n/a	n/a
16	ARID3A	chr4:129495092-129495451	HepG2	liver:	n/a	n/a
17	NFIC	chr4:129494753-129495324	SK-N-SH	brain:	n/a	n/a
18	ATF3	chr4:129494837-129495484	A549	lung:	n/a	n/a
19	USF1	chr4:129494871-129495385	A549	lung:	n/a	n/a
20	ATF3	chr4:129494768-129495508	A549	lung:	n/a	n/a
21	NR3C1	chr4:129494882-129495448	A549	lung:	n/a	chr4:129495200-129495226
22	EP300	chr4:129494748-129495422	SK-N-SH	brain:	n/a	n/a
23	NR3C1	chr4:129494859-129495388	A549	lung:	n/a	chr4:129495200-129495226
24	MAX	chr4:129494700-129495620	A549	lung:	n/a	n/a
25	SIX5	chr4:129494733-129495557	A549	lung:	n/a	chr4:129495169-129495183
26	NR3C1	chr4:129494822-129495400	A549	lung:	n/a	chr4:129495200-129495226
27	FOSL2	chr4:129494772-129495345	SK-N-SH	brain:	n/a	n/a
28	ZBTB33	chr4:129494882-129495367	A549	lung:	n/a	n/a
29	SP1	chr4:129494557-129496269	A549	lung:	n/a	n/a
30	BCL3	chr4:129494701-129495615	A549	lung:	n/a	n/a
31	REST	chr4:129494762-129495620	A549	lung:	n/a	n/a
32	GATA3	chr4:129494510-129496178	A549	lung:	n/a	n/a
33	MAFK	chr4:129494925-129495259	IMR90	lung:	n/a	n/a
34	CEBPB	chr4:129494743-129495595	A549	lung:	n/a	n/a
35	GATA3	chr4:129494852-129495477	SK-N-SH	brain:	n/a	n/a
36	PBX3	chr4:129494890-129495297	SK-N-SH	brain:	n/a	n/a
37	JUND	chr4:129494797-129495456	A549	lung:	n/a	n/a
38	FOSL2	chr4:129494482-129495633	A549	lung:	n/a	n/a
39	FOXA2	chr4:129494786-129495459	A549	lung:	n/a	n/a
40	CREB1	chr4:129494989-129495394	A549	lung:	n/a	n/a
41	EP300	chr4:129494518-129496276	A549	lung:	n/a	chr4:129495762-129495776 chr4:129494642-129494656
42	RAD21	chr4:129494911-129495252	IMR90	lung:	n/a	n/a
43	CTCF	chr4:129494838-129496470	A549	lung:	n/a	chr4:129495968-129495981 chr4:129495966-129495982 chr4:129495968-129495977 chr4:129495965-129495978 chr4:129495967-129495988 chr4:129495965-129495983
44	SP1	chr4:129494626-129496209	A549	lung:	n/a	n/a
45	ETS1	chr4:129494896-129495389	A549	lung:	n/a	n/a
46	POLR2A	chr4:129494880-129495324	SK-N-SH	brain:	n/a	n/a
47	TCF12	chr4:129494771-129495469	SK-N-SH	brain:	n/a	n/a
48	TEAD4	chr4:129494977-129495289	ECC-1	luminal epithelium:	n/a	n/a
49	GATA3	chr4:129494778-129495452	SK-N-SH	brain:	n/a	n/a
50	FOSL2	chr4:129494845-129495375	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:129492013..129498119-chr4:129729678..129735945,8	K562	blood:
2	chr4:129488347..129490310-chr4:129494247..129495821,2	MCF-7	breast:
3	chr4:129492118..129498184-chr4:129729905..129734294,8	MCF-7	breast:
4	chr4:129491971..129500938-chr4:129730367..129735945,15	K562	blood:
5	chr4:129494330..129496014-chr4:129729922..129732256,2	MCF-7	breast:
6	chr4:129494838..129497482-chr4:129516875..129519150,2	K562	blood:
7	chr4:129374210..129376419-chr4:129494420..129495998,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248187	TF binding region
ENSG00000251432	Chromatin interaction
ENSG00000077684	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17013484	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4518265	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs57357435	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58160513	0.93[EUR][1000 genomes]
rs58200674	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59261281	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60593095	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60917665	0.90[EUR][1000 genomes]
rs60972557	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932244	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72932252	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72932254	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932256	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932257	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1017672	chr4:129450450-129603977	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129482800-129498200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:129487400-129496200	Enhancers	NHDF-Ad	bronchial
3	chr4:129490000-129495800	Enhancers	NHLF	lung
4	chr4:129490000-129496200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr4:129490600-129499600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:129490800-129495600	Enhancers	HUVEC	blood vessel
7	chr4:129491200-129496200	Enhancers	NH-A	brain
8	chr4:129491400-129496200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:129491400-129496400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:129491600-129495400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:129491600-129495800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:129492200-129495400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:129492600-129497200	Enhancers	Fetal Intestine Large	intestine
14	chr4:129493200-129503600	Weak transcription	K562	blood
15	chr4:129493600-129495600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:129493600-129495800	Enhancers	HSMM	muscle
17	chr4:129493600-129496200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:129493800-129495400	Enhancers	Aorta	Aorta
19	chr4:129493800-129495400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr4:129493800-129495600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:129493800-129495800	Enhancers	HepG2	liver
22	chr4:129493800-129496000	Enhancers	HSMMtube	muscle
23	chr4:129493800-129496200	Enhancers	Ovary	ovary
24	chr4:129493800-129497000	Enhancers	Duodenum Mucosa	Duodenum
25	chr4:129494000-129495400	Enhancers	Stomach Mucosa	stomach
26	chr4:129494000-129495600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:129494200-129495400	Enhancers	Fetal Kidney	kidney
28	chr4:129494200-129495800	Enhancers	Adipose Nuclei	Adipose
29	chr4:129494200-129496000	Enhancers	Liver	Liver
30	chr4:129494200-129496200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr4:129494200-129496400	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr4:129494400-129495400	Enhancers	Fetal Muscle Leg	muscle
33	chr4:129494400-129496000	Weak transcription	Psoas Muscle	Psoas
34	chr4:129494400-129496400	Weak transcription	Right Atrium	heart
35	chr4:129494600-129495800	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr4:129494600-129496000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:129494600-129496000	Weak transcription	Pancreas	Pancrea
38	chr4:129494600-129496400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:129494800-129495400	Enhancers	A549	lung
40	chr4:129494800-129495600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:129494800-129495600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr4:129494800-129496200	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:129494800-129496400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:129494800-129499000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:129495000-129495800	Enhancers	Stomach Smooth Muscle	stomach
46	chr4:129495000-129496000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:129495000-129496000	Weak transcription	Fetal Intestine Small	intestine
48	chr4:129495000-129496200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr4:129495200-129495400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:129495200-129495400	Flanking Active TSS	Fetal Heart	heart

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