Variant report

Variant	rs2099452
Chromosome Location	chr4:54459081-54459082
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	MYC	chr4:54458889-54459525	K562	blood:	n/a	n/a
2	FOXA1	chr4:54458810-54459162	T-47D	breast:	n/a	n/a
3	FOXA1	chr4:54458805-54459203	T-47D	breast:	n/a	n/a
4	POLR2A	chr4:54458870-54459700	MCF10A-Er-Src	breast:	n/a	n/a
5	ELF1	chr4:54458805-54459181	MCF-7	breast:	n/a	n/a
6	POLR2A	chr4:54458978-54459145	MCF-7	breast:	n/a	n/a
7	FOXA2	chr4:54458690-54459249	A549	lung:	n/a	n/a
8	SP1	chr4:54459074-54459488	H1-hESC	embryonic stem cell:	n/a	chr4:54459407-54459416 chr4:54459406-54459418 chr4:54459403-54459417 chr4:54459408-54459422
9	TCF12	chr4:54458756-54459718	ECC-1	luminal epithelium:	n/a	chr4:54458983-54458990 chr4:54459088-54459098
10	MAX	chr4:54459055-54459518	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr4:54458896-54459648	MCF-7	breast:	n/a	n/a
12	MAZ	chr4:54458605-54459677	K562	blood:	n/a	n/a
13	SIN3A	chr4:54458472-54459559	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF1	chr4:54458922-54459249	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr4:54458168-54459753	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr4:54458957-54459552	K562	blood:	n/a	n/a
17	CTCF	chr4:54458940-54459090	HCPEpiC	choroid plexus:	n/a	n/a
18	JUND	chr4:54458871-54459699	K562	blood:	n/a	chr4:54459353-54459364
19	ZNF143	chr4:54458490-54459530	H1-hESC	embryonic stem cell:	n/a	chr4:54458629-54458648
20	HMGN3	chr4:54459007-54459500	K562	blood:	n/a	n/a
21	POLR2A	chr4:54458831-54459256	MCF-7	breast:	n/a	n/a
22	RCOR1	chr4:54458481-54459654	K562	blood:	n/a	n/a
23	GABPA	chr4:54458787-54459214	MCF-7	breast:	n/a	n/a
24	CUX1	chr4:54459067-54459408	K562	blood:	n/a	n/a
25	CEBPB	chr4:54458922-54459520	H1-hESC	embryonic stem cell:	n/a	n/a
26	MYC	chr4:54458928-54459545	MCF10A-Er-Src	breast:	n/a	n/a
27	EBF1	chr4:54459041-54459534	GM12878	blood:	n/a	chr4:54459393-54459404
28	YY1	chr4:54458860-54459166	HCT-116	colon:	n/a	n/a
29	MYC	chr4:54458962-54459607	K562	blood:	n/a	n/a
30	POLR2A	chr4:54458858-54459705	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr4:54458859-54459224	H1-hESC	embryonic stem cell:	n/a	n/a
32	SP1	chr4:54458673-54459608	H1-hESC	embryonic stem cell:	n/a	chr4:54459048-54459060 chr4:54459049-54459058 chr4:54459015-54459029 chr4:54459407-54459416 chr4:54459406-54459418 chr4:54459048-54459060 chr4:54459050-54459059 chr4:54459403-54459417 chr4:54459408-54459422 chr4:54459045-54459058 chr4:54458910-54458924 chr4:54459049-54459059
33	UBTF	chr4:54458925-54459586	K562	blood:	n/a	n/a
34	EP300	chr4:54458872-54459542	H1-hESC	embryonic stem cell:	n/a	chr4:54458950-54458959 chr4:54459053-54459069 chr4:54459026-54459040 chr4:54459268-54459282
35	MYC	chr4:54458939-54459596	H1-hESC	embryonic stem cell:	n/a	n/a
36	TCF12	chr4:54459020-54459222	H1-hESC	embryonic stem cell:	n/a	chr4:54459088-54459098
37	POLR2A	chr4:54458967-54459205	MCF-7	breast:	n/a	n/a
38	FOS	chr4:54459044-54459588	MCF10A-Er-Src	breast:	n/a	chr4:54459435-54459446 chr4:54459353-54459364
39	TBL1XR1	chr4:54459053-54459122	K562	blood:	n/a	n/a
40	POLR2A	chr4:54458801-54459255	HCT-116	colon:	n/a	n/a
41	POLR2A	chr4:54458877-54459186	H1-hESC	embryonic stem cell:	n/a	n/a
42	JUN	chr4:54457166-54459864	K562	blood:	n/a	chr4:54457728-54457737 chr4:54459353-54459364
43	EP300	chr4:54458968-54460009	K562	blood:	n/a	chr4:54459053-54459069 chr4:54459734-54459748 chr4:54459026-54459040 chr4:54459268-54459282
44	ZBTB7A	chr4:54458968-54459161	K562	blood:	n/a	n/a
45	POLR2A	chr4:54458850-54459663	K562	blood:	n/a	n/a
46	JUN	chr4:54458980-54459683	K562	blood:	n/a	chr4:54459353-54459364
47	TAF1	chr4:54458862-54459653	H1-hESC	embryonic stem cell:	n/a	n/a
48	JUN	chr4:54458998-54459646	K562	blood:	n/a	chr4:54459353-54459364
49	POLR2A	chr4:54458768-54459477	MCF10A-Er-Src	breast:	n/a	n/a
50	NFIC	chr4:54458738-54459712	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
LNX1	TF binding region
LNX1-AS2	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10517304	0.94[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10517305	0.94[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11936500	0.94[CEU][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11942048	0.94[CEU][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11945338	0.94[CEU][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12186283	0.81[YRI][hapmap]
rs17083112	0.94[CEU][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7691817	0.94[CEU][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv437918	chr4:54451175-54483569	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv879014	chr4:54451246-54461548	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54452600-54459600	Enhancers	HepG2	liver
2	chr4:54453200-54459200	Weak transcription	Osteobl	bone
3	chr4:54456000-54460000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr4:54457000-54459200	Enhancers	Fetal Lung	lung
5	chr4:54457200-54460200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:54457400-54459600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:54457400-54459800	Flanking Active TSS	NHEK	skin
8	chr4:54457600-54459800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:54457600-54460200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:54457600-54464400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:54457800-54459400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:54457800-54459800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:54458000-54459600	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:54458200-54459200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:54458400-54459200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:54458400-54459400	Weak transcription	Gastric	stomach
17	chr4:54458400-54459600	Enhancers	Left Ventricle	heart
18	chr4:54458600-54459200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:54458600-54459200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr4:54458600-54459400	Active TSS	Pancreas	Pancrea
21	chr4:54458600-54459600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr4:54458600-54459600	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr4:54458600-54459600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr4:54458600-54459600	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr4:54458600-54459600	Active TSS	Fetal Kidney	kidney
26	chr4:54458800-54459200	Flanking Active TSS	Fetal Stomach	stomach
27	chr4:54458800-54459200	Flanking Active TSS	HUVEC	blood vessel
28	chr4:54458800-54459400	Active TSS	H1 Cell Line	embryonic stem cell
29	chr4:54458800-54459400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:54458800-54459400	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr4:54458800-54459400	Active TSS	Duodenum Mucosa	Duodenum
32	chr4:54458800-54459400	Active TSS	Right Ventricle	heart
33	chr4:54458800-54459400	Active TSS	Stomach Mucosa	stomach
34	chr4:54458800-54459600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr4:54458800-54459600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr4:54458800-54459600	Active TSS	Esophagus	oesophagus
37	chr4:54458800-54459600	Flanking Active TSS	Placenta	Placenta
38	chr4:54458800-54459600	Enhancers	Small Intestine	intestine
39	chr4:54458800-54459600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr4:54458800-54459800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:54458800-54460000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr4:54458800-54460200	Flanking Active TSS	HMEC	breast
43	chr4:54459000-54459200	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr4:54459000-54459200	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr4:54459000-54459400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:54459000-54459400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:54459000-54459400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:54459000-54459400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr4:54459000-54459400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:54459000-54459400	Active TSS	Aorta	Aorta

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