Variant report

Variant	rs2276548
Chromosome Location	chr2:30369660-30369661
allele	A/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	CEBPB	chr2:30369325-30369716	K562	blood:	n/a	chr2:30369534-30369542
2	TBL1XR1	chr2:30369169-30369930	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:30369000-30370222	GM12878	blood:	n/a	n/a
4	CEBPB	chr2:30369300-30369770	K562	blood:	n/a	chr2:30369534-30369542
5	IRF1	chr2:30369231-30369961	K562	blood:	n/a	chr2:30369765-30369779 chr2:30369534-30369543 chr2:30369708-30369722 chr2:30369565-30369579 chr2:30369669-30369683
6	JUND	chr2:30369315-30369951	HepG2	liver:	n/a	chr2:30369764-30369773 chr2:30369425-30369437 chr2:30369427-30369435 chr2:30369425-30369436 chr2:30369532-30369541
7	MYBL2	chr2:30369076-30369852	HepG2	liver:	n/a	n/a
8	CEBPB	chr2:30369225-30369825	ECC-1	luminal epithelium:	n/a	chr2:30369534-30369542
9	MAZ	chr2:30369093-30370122	HepG2	liver:	n/a	n/a
10	ELK1	chr2:30369078-30369715	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:30368744-30370075	GM12891	blood:	n/a	n/a
12	SP1	chr2:30369087-30369942	GM12878	blood:	n/a	chr2:30369566-30369576 chr2:30369669-30369681 chr2:30369670-30369679 chr2:30369566-30369576 chr2:30369708-30369720 chr2:30369567-30369576 chr2:30369670-30369680 chr2:30369565-30369577 chr2:30369671-30369680 chr2:30369666-30369680 chr2:30369566-30369575 chr2:30369708-30369720 chr2:30369765-30369777 chr2:30369567-30369576 chr2:30369709-30369719 chr2:30369710-30369719 chr2:30369765-30369777 chr2:30369565-30369577 chr2:30369710-30369719 chr2:30369709-30369718 chr2:30369670-30369680 chr2:30369523-30369544 chr2:30369615-30369626 chr2:30369565-30369576 chr2:30369766-30369775 chr2:30369767-30369776 chr2:30369709-30369719 chr2:30369671-30369680 chr2:30369762-30369776 chr2:30369669-30369681
13	TCF7L2	chr2:30369207-30370953	HCT-116	colon:	n/a	chr2:30369426-30369435
14	HDAC2	chr2:30369155-30369797	HepG2	liver:	n/a	n/a
15	MAX	chr2:30369072-30370003	MCF-7	breast:	n/a	n/a
16	CEBPB	chr2:30369173-30369861	IMR90	lung:	n/a	chr2:30369534-30369542
17	FOS	chr2:30369309-30369880	K562	blood:	n/a	chr2:30369764-30369773 chr2:30369425-30369437 chr2:30369427-30369435 chr2:30369532-30369541 chr2:30369425-30369436
18	MAX	chr2:30369241-30369842	K562	blood:	n/a	n/a
19	USF1	chr2:30369293-30369891	HepG2	liver:	n/a	n/a
20	ZNF143	chr2:30368968-30370255	GM12878	blood:	n/a	chr2:30370111-30370121 chr2:30370242-30370252
21	CREB1	chr2:30369027-30370080	H1-hESC	embryonic stem cell:	n/a	n/a
22	EBF1	chr2:30369167-30369819	GM12878	blood:	n/a	n/a
23	ATF2	chr2:30369062-30369768	GM12878	blood:	n/a	n/a
24	TBP	chr2:30369112-30370014	GM12878	blood:	n/a	n/a
25	RFX5	chr2:30369151-30369941	HepG2	liver:	n/a	chr2:30369533-30369542
26	POLR2A	chr2:30369192-30370273	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr2:30369651-30370205	GM12892	blood:	n/a	n/a
28	E2F4	chr2:30369219-30369876	MCF10A-Er-Src	breast:	n/a	chr2:30369681-30369689 chr2:30369681-30369689 chr2:30369534-30369543 chr2:30369679-30369693 chr2:30369680-30369690
29	CREB1	chr2:30369047-30370138	GM12878	blood:	n/a	n/a
30	BHLHE40	chr2:30368862-30370056	K562	blood:	n/a	n/a
31	POLR2A	chr2:30369134-30370048	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr2:30369184-30370262	HUVEC	blood vessel:	n/a	n/a
33	YY1	chr2:30369556-30370573	K562	blood:	n/a	chr2:30370252-30370261 chr2:30370241-30370255 chr2:30370287-30370296 chr2:30370247-30370261
34	CHD2	chr2:30369186-30370064	HepG2	liver:	n/a	chr2:30369572-30369582 chr2:30369567-30369577
35	RFX5	chr2:30369162-30369858	GM12878	blood:	n/a	chr2:30369533-30369542
36	SP2	chr2:30369292-30369697	K562	blood:	n/a	chr2:30369669-30369678 chr2:30369466-30369481
37	CREB1	chr2:30369035-30370083	A549	lung:	n/a	n/a
38	PML	chr2:30369222-30370070	K562	blood:	n/a	n/a
39	EP300	chr2:30369181-30369684	HepG2	liver:	n/a	chr2:30369604-30369620
40	ZNF143	chr2:30369252-30369854	K562	blood:	n/a	n/a
41	MXI1	chr2:30369215-30369778	K562	blood:	n/a	n/a
42	FOSL2	chr2:30369046-30369663	A549	lung:	n/a	chr2:30369425-30369437 chr2:30369427-30369435 chr2:30369532-30369541
43	MAX	chr2:30369053-30370335	ECC-1	luminal epithelium:	n/a	n/a
44	NFIC	chr2:30369262-30369696	HepG2	liver:	n/a	n/a
45	ZBTB7A	chr2:30369215-30369995	HepG2	liver:	n/a	chr2:30369669-30369676
46	POLR2A	chr2:30369043-30371412	GM12878	blood:	n/a	n/a
47	POLR2A	chr2:30369112-30370093	HCT-116	colon:	n/a	n/a
48	MAX	chr2:30369128-30369934	ECC-1	luminal epithelium:	n/a	n/a
49	SIN3AK20	chr2:30369249-30369927	HepG2	liver:	n/a	n/a
50	HDAC2	chr2:30369262-30369670	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:30361445..30366413-chr2:30367443..30370864,6	MCF-7	breast:
2	chr2:30362220..30364424-chr2:30369262..30372123,2	K562	blood:
3	chr2:30368663..30370783-chr2:30453321..30456156,2	K562	blood:
4	chr2:30366474..30375732-chr2:30375765..30384167,14	MCF-7	breast:
5	chr2:30337518..30339089-chr2:30368226..30369771,2	K562	blood:
6	chr2:30357579..30360858-chr2:30368602..30370618,3	MCF-7	breast:
7	chr2:30369470..30372362-chr2:30669050..30670728,2	MCF-7	breast:

Variant related genes	Relation type
YPEL5	TF binding region
ENSG00000233862	TF binding region
ENSG00000119801	Chromatin interaction
ENSG00000172954	Chromatin interaction
ENSG00000233862	Chromatin interaction
ENSG00000213626	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11127257	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11127258	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1137288	0.83[EUR][1000 genomes]
rs11688623	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11690964	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11903016	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12620501	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12991494	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13017699	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17734800	0.87[ASN][1000 genomes]
rs17734815	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2361753	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34125526	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34350694	0.92[ASN][1000 genomes]
rs35466989	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35640159	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3768667	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4465805	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55869928	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62141084	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62141087	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62141088	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6747196	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7600457	0.83[EUR][1000 genomes]
rs7603324	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv1794716	chr2:30356661-30370785	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3373211	chr2:30368973-30372021	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3346985	chr2:30369298-30371696	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30368600-30370800	Active TSS	Fetal Brain Female	brain
2	chr2:30368600-30371200	Active TSS	Brain Angular Gyrus	brain
3	chr2:30368800-30369800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:30368800-30371000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:30368800-30371000	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr2:30368800-30371200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr2:30368800-30371200	Active TSS	Brain Anterior Caudate	brain
8	chr2:30369000-30369800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr2:30369000-30369800	Active TSS	Brain Germinal Matrix	brain
10	chr2:30369000-30370000	Active TSS	Fetal Brain Male	brain
11	chr2:30369000-30371000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:30369000-30371000	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr2:30369000-30371000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:30369000-30371000	Active TSS	Brain Substantia Nigra	brain
15	chr2:30369000-30371000	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr2:30369000-30371000	Active TSS	Fetal Intestine Small	intestine
17	chr2:30369000-30371000	Active TSS	Stomach Mucosa	stomach
18	chr2:30369000-30371200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:30369000-30371200	Active TSS	Aorta	Aorta
20	chr2:30369000-30371200	Active TSS	Left Ventricle	heart
21	chr2:30369000-30371200	Active TSS	Ovary	ovary
22	chr2:30369000-30371200	Active TSS	Pancreas	Pancrea
23	chr2:30369000-30371200	Active TSS	Psoas Muscle	Psoas
24	chr2:30369000-30371400	Active TSS	H9 Cell Line	embryonic stem cell
25	chr2:30369000-30371400	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr2:30369000-30371400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:30369000-30371400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:30369000-30371400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr2:30369000-30371400	Active TSS	Right Atrium	heart
30	chr2:30369000-30371400	Active TSS	Right Ventricle	heart
31	chr2:30369000-30371600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:30369000-30371600	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr2:30369000-30372800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr2:30369200-30369800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:30369200-30370800	Active TSS	Primary B cells from cord blood	blood
36	chr2:30369200-30370800	Active TSS	Primary T cells fromperipheralblood	blood
37	chr2:30369200-30370800	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr2:30369200-30370800	Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr2:30369200-30370800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr2:30369200-30371000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:30369200-30371000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr2:30369200-30371000	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr2:30369200-30371000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:30369200-30371000	Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr2:30369200-30371000	Active TSS	Primary B cells from peripheral blood	blood
46	chr2:30369200-30371000	Active TSS	Primary T cells from cord blood	blood
47	chr2:30369200-30371000	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr2:30369200-30371000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:30369200-30371000	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr2:30369200-30371000	Active TSS	Cortex derived primary cultured neurospheres	brain

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