Variant report

Variant	rs57989706
Chromosome Location	chr12:58005028-58005029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:108)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:108 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr12:58004970-58005284	K562	blood:	n/a	n/a
2	POLR2A	chr12:58004765-58005560	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr12:58004955-58005510	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:58004756-58005632	U87	brain:	n/a	n/a
5	CTCF	chr12:58005020-58005170	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr12:58004862-58005500	GM19099	blood:	n/a	n/a
7	IRF1	chr12:58004934-58005443	K562	blood:	n/a	chr12:58005158-58005172 chr12:58005179-58005193
8	POLR2A	chr12:58004756-58005576	U87	brain:	n/a	n/a
9	POLR2A	chr12:58004997-58005387	HUVEC	blood vessel:	n/a	n/a
10	MAX	chr12:58004759-58005695	HepG2	liver:	n/a	chr12:58005549-58005559 chr12:58005577-58005587 chr12:58005016-58005026 chr12:58005375-58005385
11	HDAC2	chr12:58004986-58005236	K562	blood:	n/a	n/a
12	POLR2A	chr12:58004974-58005478	U87	brain:	n/a	n/a
13	MAX	chr12:58004874-58005358	SK-N-SH	brain:	n/a	chr12:58005016-58005026
14	POLR2A	chr12:58005028-58005435	GM18526	blood:	n/a	n/a
15	MAX	chr12:58004860-58005405	SK-N-SH	brain:	n/a	chr12:58005016-58005026 chr12:58005375-58005385
16	TCF12	chr12:58004836-58005588	A549	lung:	n/a	n/a
17	RCOR1	chr12:58004885-58005453	K562	blood:	n/a	n/a
18	REST	chr12:58004932-58005669	H1-neurons	neurons:	n/a	chr12:58005549-58005562 chr12:58005156-58005169 chr12:58005221-58005239
19	E2F6	chr12:58004234-58005187	H1-hESC	embryonic stem cell:	n/a	chr12:58004752-58004762 chr12:58005116-58005128
20	ZBTB7A	chr12:58005023-58005860	K562	blood:	n/a	n/a
21	POLR2A	chr12:58004979-58005477	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:58004901-58005531	PFSK-1	brain:	n/a	n/a
23	TCF12	chr12:58004670-58005549	ECC-1	luminal epithelium:	n/a	n/a
24	CHD2	chr12:58004509-58005234	K562	blood:	n/a	n/a
25	ZBTB7A	chr12:58004602-58006076	ECC-1	luminal epithelium:	n/a	n/a
26	HEY1	chr12:58004910-58005587	HepG2	liver:	n/a	chr12:58004993-58005008
27	MXI1	chr12:58004136-58006760	SK-N-SH	brain:	n/a	n/a
28	MAX	chr12:58004963-58005297	K562	blood:	n/a	chr12:58005016-58005026
29	CEBPD	chr12:58004985-58005704	HepG2	liver:	n/a	n/a
30	HEY1	chr12:58004988-58005564	K562	blood:	n/a	chr12:58004993-58005008
31	TAF1	chr12:58004972-58005508	HepG2	liver:	n/a	n/a
32	E2F6	chr12:58004957-58005329	K562	blood:	n/a	chr12:58005116-58005128
33	POLR2A	chr12:58004979-58005426	A549	lung:	n/a	n/a
34	POLR2A	chr12:58004943-58005416	Gliobla	brain:	n/a	n/a
35	POLR2A	chr12:58005013-58005459	PANC-1	pancreas:	n/a	n/a
36	YY1	chr12:58005016-58005417	K562	blood:	n/a	chr12:58005032-58005043 chr12:58005199-58005208
37	POLR2A	chr12:58004810-58005646	HepG2	liver:	n/a	n/a
38	ZBTB7A	chr12:58004757-58005872	K562	blood:	n/a	n/a
39	POLR2A	chr12:58004970-58005537	ProgFib	skin:	n/a	n/a
40	POLR2A	chr12:58005009-58005444	H1-neurons	neurons:	n/a	n/a
41	CHD2	chr12:58004867-58005360	GM12878	blood:	n/a	n/a
42	PML	chr12:58004986-58005456	K562	blood:	n/a	n/a
43	BHLHE40	chr12:58004900-58005056	K562	blood:	n/a	n/a
44	TAF1	chr12:58004751-58005607	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr12:58004885-58005506	A549	lung:	n/a	n/a
46	POLR2A	chr12:58004948-58005397	A549	lung:	n/a	n/a
47	FOXP2	chr12:58005022-58005223	SK-N-MC	brain:	n/a	n/a
48	SIN3A	chr12:58002857-58005570	H1-hESC	embryonic stem cell:	n/a	chr12:58004864-58004877
49	POLR2A	chr12:58004897-58005579	GM15510	blood:	n/a	n/a
50	MAX	chr12:58004878-58005405	H1-hESC	embryonic stem cell:	n/a	chr12:58005016-58005026 chr12:58005375-58005385

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58004992-58005042	GM12878	blood:	n/a
2	chr12:58004992-58005042	NHBE	bronchial:	n/a
3	chr12:58004992-58005042	AG10803	skin:	n/a
4	chr12:58004992-58005042	MCF-7	breast:	n/a
5	chr12:58004992-58005042	IMR90	lung:	fetal
6	chr12:58004992-58005042	NH-A	brain:	n/a
7	chr12:58004992-58005042	HRE	kidney:	n/a
8	chr12:58004992-58005042	T-47D	breast:	n/a
9	chr12:58004992-58005042	Hela-S3	cervix:	n/a
10	chr12:58004992-58005042	ECC-1	luminal epithelium:	n/a
11	chr12:58004992-58005042	LNCaP	prostate:	n/a
12	chr12:58004992-58005042	Caco-2	colon:	n/a
13	chr12:58004992-58005042	GM12891	blood:	n/a
14	chr12:58004992-58005042	SKMC	muscle:	n/a
15	chr12:58004992-58005042	PANC-1	pancreas:	n/a
16	chr12:58004992-58005042	ProgFib	skin:	n/a
17	chr12:58004992-58005042	Hepatocyte	liver:	n/a
18	chr12:58004992-58005042	AG09309	skin:	n/a
19	chr12:58004992-58005042	HPAEpiC	pulmonary alveolar:	n/a
20	chr12:58004992-58005042	AG09319	gingival:	n/a
21	chr12:58004992-58005042	CMK	blood:	n/a
22	chr12:58004992-58005042	HMEC	breast:	n/a
23	chr12:58004992-58005042	PFSK-1	brain:	n/a
24	chr12:58004992-58005042	AG04449	skin:	fetal
25	chr12:58004992-58005042	HEEpiC	esophagus:	n/a
26	chr12:58004992-58005042	HCM	heart:	n/a
27	chr12:58004992-58005042	A549	lung:	n/a
28	chr12:58004992-58005042	H1-hESC	embryonic stem cell:	embryo
29	chr12:58004992-58005042	NHDF-neo	bronchial:	n/a
30	chr12:58004992-58005042	MCF10A-Er-Src	breast:	n/a
31	chr12:58004992-58005042	RPTEC	kidney:	n/a
32	chr12:58004992-58005042	NB4	blood:	n/a
33	chr12:58004992-58005042	HCPEpiC	choroid plexus:	n/a
34	chr12:58004992-58005042	SAEC	small airway:	n/a
35	chr12:58004992-58005042	SK-N-MC	brain:	n/a
36	chr12:58004992-58005042	HL-60	blood:	n/a
37	chr12:58004992-58005042	K562	blood:	n/a
38	chr12:58004992-58005042	HCF	heart:	n/a
39	chr12:58004992-58005042	HEK293	kidney:	embryo
40	chr12:58004992-58005042	BJ	skin:	n/a
41	chr12:58004992-58005042	GM06990	blood:	n/a
42	chr12:58004992-58005042	HUVEC	blood vessel:	n/a
43	chr12:58004992-58005042	U87	brain:	n/a
44	chr12:58004992-58005042	BE2_C	brain:	n/a
45	chr12:58004992-58005042	AG04450	lung:	fetal
46	chr12:58004992-58005042	NT2-D1	testis:	n/a
47	chr12:58004992-58005042	HRCEpiC	kidney:	n/a
48	chr12:58004992-58005042	HNPCEpiC	eye:	n/a
49	chr12:58004992-58005042	AoSMC	blood vessel:	n/a
50	chr12:58004992-58005042	HepG2	liver:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58004618..58008024-chr12:58024930..58028098,5	MCF-7	breast:
2	chr12:57912257..57915408-chr12:58000825..58006358,4	K562	blood:
3	chr12:57930705..57935401-chr12:58001977..58005950,4	K562	blood:
4	chr12:57911699..57918406-chr12:58000825..58010019,18	K562	blood:
5	chr12:58002964..58008004-chr12:58117447..58122099,5	MCF-7	breast:
6	chr12:58004396..58008788-chr12:58163385..58167140,4	MCF-7	breast:
7	chr12:58003448..58005159-chr12:58329612..58331307,2	K562	blood:

No data

Variant related genes	Relation type
ARHGEF25	TF binding region
ARHGEF25	CpG island
ENSG00000135454	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000257698	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000037897	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs57624896	0.90[AFR][1000 genomes]
rs58060255	0.81[AFR][1000 genomes]
rs59166749	0.91[AFR][1000 genomes]
rs59193499	0.90[AFR][1000 genomes]
rs73335926	0.90[AFR][1000 genomes]
rs73335930	0.90[AFR][1000 genomes]
rs73335931	0.90[AFR][1000 genomes]
rs73338203	0.90[AFR][1000 genomes]
rs73346063	0.81[AFR][1000 genomes]
rs73346089	1.00[AFR][1000 genomes]
rs73346092	1.00[AFR][1000 genomes]
rs73347951	0.90[AFR][1000 genomes]
rs73349943	0.90[AFR][1000 genomes]
rs73351685	0.90[AFR][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	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58003000-58005800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:58003200-58005800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr12:58003200-58005800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr12:58003400-58005800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr12:58003400-58006000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:58003400-58006000	Active TSS	Fetal Kidney	kidney
7	chr12:58003600-58006000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr12:58003600-58006000	Active TSS	Colon Smooth Muscle	Colon
9	chr12:58003600-58006000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
10	chr12:58003600-58006000	Active TSS	Ovary	ovary
11	chr12:58003800-58005200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:58003800-58005200	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr12:58003800-58005400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
14	chr12:58003800-58005800	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr12:58003800-58005800	Active TSS	Aorta	Aorta
16	chr12:58003800-58005800	Enhancers	Fetal Brain Male	brain
17	chr12:58003800-58005800	Active TSS	Right Atrium	heart
18	chr12:58003800-58006000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:58003800-58006400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:58003800-58006400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr12:58004000-58006400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr12:58004200-58005200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:58004200-58005200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr12:58004200-58005400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
25	chr12:58004200-58005400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:58004200-58005400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:58004200-58005400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
28	chr12:58004200-58005400	Bivalent Enhancer	Liver	Liver
29	chr12:58004200-58005400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
30	chr12:58004200-58005400	Bivalent/Poised TSS	NHEK	skin
31	chr12:58004200-58005600	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr12:58004200-58005600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr12:58004200-58005800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr12:58004200-58006000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr12:58004200-58006000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
36	chr12:58004200-58006000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:58004200-58006200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
38	chr12:58004200-58006400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:58004400-58005200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr12:58004400-58005200	Flanking Active TSS	Osteobl	bone
41	chr12:58004400-58005400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:58004400-58005600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
43	chr12:58004400-58005600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
44	chr12:58004400-58006000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
45	chr12:58004400-58006000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:58004400-58006000	Active TSS	Brain Substantia Nigra	brain
47	chr12:58004400-58006200	Active TSS	Brain Angular Gyrus	brain
48	chr12:58004400-58006200	Active TSS	Left Ventricle	heart
49	chr12:58004600-58005200	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:58004600-58005200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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