Variant report

Variant	rs542391006
Chromosome Location	chr1:151583816-151583817
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	ZNF143	chr1:151583810-151584814	Hela-S3	cervix:	n/a	chr1:151584458-151584476 chr1:151584462-151584481 chr1:151584366-151584375 chr1:151584460-151584469 chr1:151584458-151584467 chr1:151584364-151584382 chr1:151584364-151584373
2	NR3C1	chr1:151583736-151584190	A549	lung:	n/a	n/a
3	SRF	chr1:151583801-151584083	HepG2	liver:	n/a	n/a
4	BHLHE40	chr1:151583721-151584734	HepG2	liver:	n/a	n/a
5	ARID3A	chr1:151583773-151584484	K562	blood:	n/a	n/a
6	SREBP1	chr1:151583792-151584923	GM12878	blood:	n/a	n/a
7	TBP	chr1:151583773-151584543	HepG2	liver:	n/a	n/a
8	STAT3	chr1:151583791-151584475	MCF10A-Er-Src	breast:	n/a	n/a
9	MAX	chr1:151583767-151584946	Hela-S3	cervix:	n/a	chr1:151584441-151584451
10	REST	chr1:151583712-151584414	HL-60	blood:	n/a	n/a
11	CEBPB	chr1:151583720-151584418	K562	blood:	n/a	chr1:151583999-151584010 chr1:151584231-151584244 chr1:151583997-151584008 chr1:151583999-151584008
12	CEBPB	chr1:151583632-151584821	MCF-7	breast:	n/a	chr1:151583999-151584010 chr1:151584231-151584244 chr1:151583997-151584008 chr1:151583999-151584008
13	EGR1	chr1:151583675-151585014	MCF-7	breast:	n/a	chr1:151584247-151584260 chr1:151584502-151584516 chr1:151584457-151584481 chr1:151584438-151584451 chr1:151584438-151584451 chr1:151584439-151584448 chr1:151584438-151584451 chr1:151584442-151584452 chr1:151584363-151584387 chr1:151584438-151584448 chr1:151584437-151584452 chr1:151584438-151584451 chr1:151584247-151584257 chr1:151584437-151584451 chr1:151584439-151584450
14	USF2	chr1:151583683-151584476	Hela-S3	cervix:	n/a	chr1:151583962-151583973
15	CEBPB	chr1:151583688-151584485	Hela-S3	cervix:	n/a	chr1:151583999-151584010 chr1:151584231-151584244 chr1:151583997-151584008 chr1:151583999-151584008
16	USF2	chr1:151583721-151584099	HepG2	liver:	n/a	chr1:151583962-151583973
17	FOXA1	chr1:151583682-151584205	HepG2	liver:	n/a	n/a
18	NR3C1	chr1:151583764-151584046	A549	lung:	n/a	n/a
19	MAX	chr1:151583757-151584131	K562	blood:	n/a	n/a
20	FOXA1	chr1:151583721-151584044	HepG2	liver:	n/a	n/a
21	CEBPB	chr1:151583583-151584431	MCF-7	breast:	n/a	chr1:151583999-151584010 chr1:151584231-151584244 chr1:151583997-151584008 chr1:151583999-151584008
22	USF1	chr1:151583667-151584193	A549	lung:	n/a	chr1:151583963-151583974
23	MAFK	chr1:151583794-151584499	Hela-S3	cervix:	n/a	n/a
24	GTF2F1	chr1:151583813-151584536	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr1:151583780-151583930	HEK293	kidney:	n/a	n/a
26	SIX5	chr1:151583737-151584806	A549	lung:	n/a	chr1:151584364-151584373 chr1:151584362-151584376 chr1:151584458-151584467 chr1:151584456-151584470 chr1:151584460-151584469 chr1:151584366-151584375
27	CEBPB	chr1:151583809-151584251	ECC-1	luminal epithelium:	n/a	chr1:151583999-151584010 chr1:151584231-151584244 chr1:151583997-151584008 chr1:151583999-151584008
28	CTCF	chr1:151583780-151583930	MCF-7	breast:	n/a	n/a
29	SRF	chr1:151583795-151584039	HepG2	liver:	n/a	n/a
30	CEBPB	chr1:151583785-151584201	K562	blood:	n/a	chr1:151583999-151584010 chr1:151583997-151584008 chr1:151583999-151584008
31	MAX	chr1:151583597-151585659	A549	lung:	n/a	chr1:151584441-151584451
32	EP300	chr1:151583723-151584205	Hela-S3	cervix:	n/a	chr1:151584167-151584175
33	HCFC1	chr1:151583005-151585633	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr1:151583647-151584690	HL-60	blood:	n/a	n/a
35	RXRA	chr1:151583774-151584110	HepG2	liver:	n/a	n/a
36	ELF1	chr1:151583726-151584775	MCF-7	breast:	n/a	n/a
37	FOS	chr1:151583656-151584402	MCF10A-Er-Src	breast:	n/a	chr1:151584248-151584257 chr1:151584247-151584256
38	USF1	chr1:151583807-151584079	HepG2	liver:	n/a	chr1:151583963-151583974
39	BRCA1	chr1:151583812-151584589	Hela-S3	cervix:	n/a	n/a
40	FOXA2	chr1:151583714-151584114	HepG2	liver:	n/a	n/a
41	MYC	chr1:151583734-151584932	MCF10A-Er-Src	breast:	n/a	chr1:151584441-151584451
42	RFX5	chr1:151583811-151584582	Hela-S3	cervix:	n/a	n/a
43	CEBPB	chr1:151583721-151584422	HepG2	liver:	n/a	chr1:151583999-151584010 chr1:151584231-151584244 chr1:151583997-151584008 chr1:151583999-151584008
44	NR3C1	chr1:151583703-151584185	A549	lung:	n/a	n/a
45	KAP1	chr1:151583778-151584551	HEK293	kidney:	n/a	n/a
46	HDAC2	chr1:151583754-151584130	HepG2	liver:	n/a	n/a
47	MAX	chr1:151583600-151584162	MCF-7	breast:	n/a	n/a
48	MAX	chr1:151583806-151585032	K562	blood:	n/a	chr1:151584441-151584451
49	ARID3A	chr1:151583740-151584707	HepG2	liver:	n/a	n/a
50	CEBPB	chr1:151583779-151584236	HepG2	liver:	n/a	chr1:151583999-151584010 chr1:151583997-151584008 chr1:151583999-151584008

No.	Distal block	Cell Line	Cell type
1	chr1:151580809..151584127-chr1:151586626..151590699,5	MCF-7	breast:
2	chr1:151534012..151536307-chr1:151581033..151583882,2	MCF-7	breast:
3	chr1:151510726..151515686-chr1:151583230..151586215,6	MCF-7	breast:
4	chr1:151583806..151586204-chr1:151610936..151612672,2	MCF-7	breast:
5	chr1:151509848..151514263-chr1:151581077..151585541,5	MCF-7	breast:
6	chr1:151430633..151432391-chr1:151583582..151586341,2	MCF-7	breast:
7	chr1:151582188..151584894-chr1:151679011..151681614,2	MCF-7	breast:
8	chr1:151583249..151586152-chr1:151761338..151763937,3	K562	blood:
9	chr1:151583782..151586135-chr6:26156499..26159013,2	MCF-7	breast:

Variant related genes	Relation type
SNX27	TF binding region
ENSG00000203288	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000182134	Chromatin interaction
ENSG00000159409	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000158373	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	esv3354758	chr1:151583553-151586301	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151580200-151584000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:151581000-151584200	Weak transcription	Fetal Stomach	stomach
3	chr1:151581200-151584200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:151581400-151584000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:151581600-151584200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:151582400-151584000	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr1:151582600-151584000	Enhancers	Placenta	Placenta
8	chr1:151582600-151584200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:151582600-151584200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:151582800-151584200	Enhancers	Fetal Intestine Small	intestine
11	chr1:151583200-151584000	Enhancers	Fetal Intestine Large	intestine
12	chr1:151583200-151584200	Enhancers	Gastric	stomach
13	chr1:151583400-151584200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr1:151583600-151584200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:151583600-151584200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:151583600-151584200	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr1:151583600-151584200	Flanking Active TSS	HepG2	liver
18	chr1:151583600-151584200	Enhancers	HSMM	muscle
19	chr1:151583600-151584200	Enhancers	NHEK	skin
20	chr1:151583600-151584400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:151583600-151584400	Enhancers	HMEC	breast
22	chr1:151583600-151584600	Enhancers	Stomach Mucosa	stomach
23	chr1:151583800-151584000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:151583800-151584000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:151583800-151584000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr1:151583800-151584000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:151583800-151584000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr1:151583800-151584000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:151583800-151584000	Enhancers	Primary B cells from cord blood	blood
30	chr1:151583800-151584000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:151583800-151584000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:151583800-151584000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr1:151583800-151584000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:151583800-151584000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:151583800-151584000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr1:151583800-151584000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:151583800-151584000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:151583800-151584000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:151583800-151584000	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr1:151583800-151584000	Enhancers	Brain Angular Gyrus	brain
41	chr1:151583800-151584000	Enhancers	Colon Smooth Muscle	Colon
42	chr1:151583800-151584000	Enhancers	Duodenum Mucosa	Duodenum
43	chr1:151583800-151584000	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr1:151583800-151584000	Enhancers	Fetal Lung	lung
45	chr1:151583800-151584000	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr1:151583800-151584000	Enhancers	Rectal Smooth Muscle	rectum
47	chr1:151583800-151584000	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr1:151583800-151584000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr1:151583800-151584000	Enhancers	HSMMtube	muscle
50	chr1:151583800-151584000	Genic enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links