Variant report

Variant	rs59927838
Chromosome Location	chr2:47597346-47597347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr2:47596834-47597458	ECC-1	luminal epithelium:	n/a	chr2:47596969-47596979 chr2:47596964-47596977
2	POLR2A	chr2:47596235-47597378	Hela-S3	cervix:	n/a	n/a
3	TEAD4	chr2:47595982-47597421	ECC-1	luminal epithelium:	n/a	n/a
4	FOS	chr2:47597166-47597415	MCF10A-Er-Src	breast:	n/a	n/a
5	E2F6	chr2:47595900-47597408	H1-hESC	embryonic stem cell:	n/a	chr2:47596969-47596978
6	MAX	chr2:47595983-47597500	HepG2	liver:	n/a	n/a
7	HA-E2F1	chr2:47595917-47597418	MCF-7	breast:	n/a	chr2:47596969-47596978
8	TCF12	chr2:47596957-47597407	H1-hESC	embryonic stem cell:	n/a	chr2:47597294-47597302
9	MAX	chr2:47595905-47597458	H1-hESC	embryonic stem cell:	n/a	n/a
10	CREB1	chr2:47596030-47597404	HepG2	liver:	n/a	n/a
11	FOS	chr2:47597122-47597410	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr2:47597148-47597347	MCF10A-Er-Src	breast:	n/a	n/a
13	TEAD4	chr2:47597012-47597362	ECC-1	luminal epithelium:	n/a	n/a
14	TCF12	chr2:47595716-47597400	MCF-7	breast:	n/a	chr2:47597294-47597302
15	POLR2A	chr2:47596136-47597389	K562	blood:	n/a	n/a
16	MAX	chr2:47595927-47597371	MCF-7	breast:	n/a	n/a
17	NFIC	chr2:47596831-47597375	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr2:47595799-47597412	HCT-116	colon:	n/a	n/a
19	ESR1	chr2:47597018-47597372	ECC-1	luminal epithelium:	n/a	n/a
20	JUND	chr2:47595916-47597404	HCT-116	colon:	n/a	chr2:47596342-47596353
21	ZEB1	chr2:47595872-47597508	HepG2	liver:	n/a	chr2:47597215-47597227 chr2:47596421-47596430
22	TCF12	chr2:47595977-47597578	ECC-1	luminal epithelium:	n/a	chr2:47597294-47597302
23	HDAC2	chr2:47595964-47597414	MCF-7	breast:	n/a	chr2:47597263-47597277
24	MAX	chr2:47595944-47597429	ECC-1	luminal epithelium:	n/a	n/a
25	CTBP2	chr2:47596148-47597467	H1-hESC	embryonic stem cell:	n/a	n/a
26	TCF12	chr2:47597049-47597360	H1-hESC	embryonic stem cell:	n/a	chr2:47597294-47597302
27	FOSL1	chr2:47595860-47597447	HCT-116	colon:	n/a	chr2:47596342-47596353 chr2:47595906-47595915
28	MAX	chr2:47595951-47597466	MCF-7	breast:	n/a	n/a
29	TCF12	chr2:47595844-47597572	ECC-1	luminal epithelium:	n/a	chr2:47597294-47597302
30	HDAC2	chr2:47597077-47597372	H1-hESC	embryonic stem cell:	n/a	chr2:47597263-47597277
31	YY1	chr2:47596041-47597351	HepG2	liver:	n/a	chr2:47597228-47597239 chr2:47596966-47596975 chr2:47596402-47596416
32	EP300	chr2:47595950-47597440	ECC-1	luminal epithelium:	n/a	chr2:47596149-47596158 chr2:47597153-47597162
33	MAX	chr2:47595989-47597370	HepG2	liver:	n/a	n/a
34	FOS	chr2:47597215-47597374	MCF10A-Er-Src	breast:	n/a	n/a
35	TAF1	chr2:47595996-47597348	ECC-1	luminal epithelium:	n/a	n/a
36	MYC	chr2:47597184-47597376	MCF10A-Er-Src	breast:	n/a	n/a
37	TAF1	chr2:47595926-47597399	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr2:47596854-47597364	K562	blood:	n/a	n/a
39	YY1	chr2:47596997-47597361	K562	blood:	n/a	chr2:47597228-47597239
40	POLR2A	chr2:47595998-47597502	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr2:47596010-47597365	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr2:47595943-47597381	HCT-116	colon:	n/a	n/a
43	EP300	chr2:47597004-47597370	H1-hESC	embryonic stem cell:	n/a	chr2:47597153-47597162
44	UBTF	chr2:47596429-47597349	K562	blood:	n/a	n/a
45	TAF1	chr2:47597124-47597366	K562	blood:	n/a	n/a
46	SIN3AK20	chr2:47595954-47597534	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:47597331-47597381	SKMC	muscle:	n/a
2	chr2:47597331-47597381	T-47D	breast:	n/a
3	chr2:47597331-47597381	U87	brain:	n/a
4	chr2:47597331-47597381	Caco-2	colon:	n/a
5	chr2:47597331-47597381	K562	blood:	n/a
6	chr2:47597331-47597381	MCF10A-Er-Src	breast:	n/a
7	chr2:47597331-47597381	AoSMC	blood vessel:	n/a
8	chr2:47597331-47597381	HEK293	kidney:	embryo
9	chr2:47597331-47597381	HIPEpiC	eye:	n/a
10	chr2:47597331-47597381	GM06990	blood:	n/a
11	chr2:47597331-47597381	MCF-7	breast:	n/a
12	chr2:47597331-47597381	HAEpiC	amniotic membrane:	n/a
13	chr2:47597331-47597381	AG09319	gingival:	n/a
14	chr2:47597331-47597381	H1-hESC	embryonic stem cell:	embryo
15	chr2:47597331-47597381	AG10803	skin:	n/a
16	chr2:47597331-47597381	IMR90	lung:	fetal
17	chr2:47597331-47597381	PFSK-1	brain:	n/a
18	chr2:47597331-47597381	A549	lung:	n/a
19	chr2:47597331-47597381	HCM	heart:	n/a
20	chr2:47597331-47597381	SK-N-SH_RA	brain:	n/a
21	chr2:47597331-47597381	NB4	blood:	n/a
22	chr2:47597331-47597381	NHBE	bronchial:	n/a
23	chr2:47597331-47597381	GM12892	blood:	n/a
24	chr2:47597331-47597381	ovcar-3	ovarian:	n/a
25	chr2:47597331-47597381	RPTEC	kidney:	n/a
26	chr2:47597331-47597381	AG04449	skin:	fetal
27	chr2:47597331-47597381	HUVEC	blood vessel:	n/a
28	chr2:47597331-47597381	AG09309	skin:	n/a
29	chr2:47597331-47597381	GM12878	blood:	n/a
30	chr2:47597331-47597381	Hela-S3	cervix:	n/a
31	chr2:47597331-47597381	HPAEpiC	pulmonary alveolar:	n/a
32	chr2:47597331-47597381	CMK	blood:	n/a
33	chr2:47597331-47597381	HRE	kidney:	n/a
34	chr2:47597331-47597381	LNCaP	prostate:	n/a
35	chr2:47597331-47597381	NHDF-neo	bronchial:	n/a
36	chr2:47597331-47597381	AG04450	lung:	fetal
37	chr2:47597331-47597381	SK-N-MC	brain:	n/a
38	chr2:47597331-47597381	BE2_C	brain:	n/a
39	chr2:47597331-47597381	SK-N-SH	brain:	n/a
40	chr2:47597331-47597381	Hepatocyte	liver:	n/a
41	chr2:47597331-47597381	HCPEpiC	choroid plexus:	n/a
42	chr2:47597331-47597381	HCT-116	colon:	n/a
43	chr2:47597331-47597381	PrEC	prostate:	n/a
44	chr2:47597331-47597381	HepG2	liver:	n/a
45	chr2:47597331-47597381	SAEC	small airway:	n/a
46	chr2:47597331-47597381	NT2-D1	testis:	n/a
47	chr2:47597331-47597381	HL-60	blood:	n/a
48	chr2:47597331-47597381	PANC-1	pancreas:	n/a
49	chr2:47597331-47597381	HCF	heart:	n/a
50	chr2:47597331-47597381	ProgFib	skin:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47570861..47572963-chr2:47596345..47598113,2	K562	blood:
2	chr2:47592763..47599978-chr2:47628456..47631890,7	K562	blood:
3	chr2:47595432..47597958-chr2:47630032..47632167,2	K562	blood:
4	chr2:47596733..47599007-chr2:47599869..47602231,2	K562	blood:
5	chr2:47401421..47404385-chr2:47596204..47598281,3	MCF-7	breast:
6	chr2:47595241..47598489-chr2:47628033..47632018,10	MCF-7	breast:
7	chr2:47560518..47577182-chr2:47592669..47600258,43	MCF-7	breast:
8	chr13:115000491..115001056-chr2:47597036..47597630,2	Hela-S3	cervix:
9	chr2:47402779..47405652-chr2:47594724..47597829,3	K562	blood:
10	chr17:62502573..62503177-chr2:47596612..47597409,2	Hela-S3	cervix:
11	chr2:47559485..47574826-chr2:47594341..47605593,65	MCF-7	breast:

No data

Variant related genes	Relation type
EPCAM	TF binding region
EPCAM	CpG island
ENSG00000258890	Chromatin interaction
ENSG00000234690	Chromatin interaction
ENSG00000095002	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000119888	Chromatin interaction
ENSG00000130177	Chromatin interaction
ENSG00000108654	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs57831950	1.00[AMR][1000 genomes]
rs57916992	1.00[AMR][1000 genomes]
rs57945178	1.00[AMR][1000 genomes]
rs58882508	1.00[AMR][1000 genomes]
rs58931241	1.00[AMR][1000 genomes]
rs59248614	1.00[AMR][1000 genomes]
rs60068970	1.00[AMR][1000 genomes]
rs60358586	1.00[AMR][1000 genomes]
rs60518577	1.00[AMR][1000 genomes]
rs60887102	1.00[AMR][1000 genomes]
rs60998282	1.00[AMR][1000 genomes]
rs61013408	0.86[AFR][1000 genomes]
rs61212083	1.00[AMR][1000 genomes]
rs61451736	1.00[AMR][1000 genomes]
rs72882704	1.00[AMR][1000 genomes]
rs72882709	1.00[AMR][1000 genomes]
rs72882712	1.00[AMR][1000 genomes]
rs72882715	1.00[AMR][1000 genomes]
rs72882770	1.00[AMR][1000 genomes]
rs72884694	1.00[AMR][1000 genomes]
rs72884701	1.00[AMR][1000 genomes]
rs72886311	1.00[AMR][1000 genomes]
rs72886331	1.00[AMR][1000 genomes]
rs72886333	1.00[AMR][1000 genomes]
rs72886340	1.00[AMR][1000 genomes]
rs72886346	1.00[AMR][1000 genomes]
rs72886357	1.00[AMR][1000 genomes]
rs72886367	1.00[AMR][1000 genomes]
rs72888235	1.00[AMR][1000 genomes]
rs72888241	1.00[AMR][1000 genomes]
rs72888249	1.00[AMR][1000 genomes]
rs72888257	1.00[AMR][1000 genomes]
rs72888260	1.00[AMR][1000 genomes]
rs72888262	1.00[AMR][1000 genomes]
rs72888268	1.00[AMR][1000 genomes]
rs72888274	1.00[AMR][1000 genomes]
rs72888288	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1009586	chr2:47552706-47621487	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
6	nsv520660	chr2:47590034-47601106	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47595800-47598000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr2:47595800-47598200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:47595800-47598400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr2:47595800-47599200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr2:47596000-47597400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:47596000-47597400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:47596000-47597400	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr2:47596000-47597400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:47596000-47597400	Active TSS	Brain Anterior Caudate	brain
10	chr2:47596000-47597400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
11	chr2:47596000-47597400	Active TSS	Brain Substantia Nigra	brain
12	chr2:47596000-47597400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
13	chr2:47596000-47597400	Bivalent Enhancer	Fetal Brain Male	brain
14	chr2:47596000-47597400	Bivalent/Poised TSS	Fetal Brain Female	brain
15	chr2:47596000-47597400	Flanking Active TSS	HMEC	breast
16	chr2:47596000-47597400	Bivalent/Poised TSS	Osteobl	bone
17	chr2:47596000-47597600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr2:47596000-47597600	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr2:47596000-47597600	Active TSS	Fetal Intestine Small	intestine
20	chr2:47596000-47598000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr2:47596000-47598000	Active TSS	Pancreas	Pancrea
22	chr2:47596000-47599000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr2:47596000-47599000	Active TSS	Fetal Kidney	kidney
24	chr2:47596000-47599400	Active TSS	K562	blood
25	chr2:47596000-47601000	Active TSS	Rectal Smooth Muscle	rectum
26	chr2:47596200-47597400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:47596200-47597400	Active TSS	Gastric	stomach
28	chr2:47596200-47598000	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr2:47596200-47598200	Active TSS	Duodenum Mucosa	Duodenum
30	chr2:47596400-47597400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
31	chr2:47596400-47597400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
32	chr2:47596400-47597400	Bivalent/Poised TSS	HSMM	muscle
33	chr2:47596600-47597400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr2:47596600-47597400	Bivalent/Poised TSS	HepG2	liver
35	chr2:47596600-47600400	Active TSS	Small Intestine	intestine
36	chr2:47596800-47597400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
37	chr2:47596800-47597400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
38	chr2:47596800-47597400	Bivalent/Poised TSS	Psoas Muscle	Psoas
39	chr2:47596800-47597400	Active TSS	Hela-S3	cervix
40	chr2:47596800-47600000	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr2:47597000-47597400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:47597000-47597400	Bivalent Enhancer	Primary B cells from cord blood	blood
43	chr2:47597000-47597400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
44	chr2:47597000-47597400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:47597000-47597400	Bivalent/Poised TSS	Colonic Mucosa	Colon
46	chr2:47597000-47597400	Enhancers	Spleen	Spleen
47	chr2:47597000-47597600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:47597000-47598200	Active TSS	Stomach Mucosa	stomach
49	chr2:47597000-47600600	Weak transcription	A549	lung
50	chr2:47597200-47597400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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