Variant report

Variant	rs542208897
Chromosome Location	chr12:31742676-31742677
allele	-/AAC
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	MYBL2	chr12:31742661-31743335	HepG2	liver:	n/a	n/a
2	MAFK	chr12:31742673-31743165	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:31742347-31744772	IMR90	lung:	n/a	n/a
4	SIN3AK20	chr12:31742497-31743362	MCF-7	breast:	n/a	n/a
5	POLR2A	chr12:31742595-31744836	GM19193	blood:	n/a	n/a
6	EP300	chr12:31742538-31743254	A549	lung:	n/a	chr12:31743067-31743083 chr12:31743015-31743031 chr12:31743063-31743079
7	RFX5	chr12:31742532-31743294	HepG2	liver:	n/a	n/a
8	NFIC	chr12:31742169-31743119	GM12878	blood:	n/a	n/a
9	STAT5A	chr12:31742587-31743652	GM12878	blood:	n/a	chr12:31742787-31742799
10	YY1	chr12:31742674-31743481	GM12891	blood:	n/a	chr12:31743295-31743309 chr12:31743082-31743096 chr12:31742789-31742800 chr12:31743076-31743087 chr12:31743243-31743257 chr12:31743166-31743177 chr12:31743435-31743449
11	POLR2A	chr12:31742607-31744526	HepG2	liver:	n/a	n/a
12	TBL1XR1	chr12:31742612-31743642	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:31742606-31744703	NB4	blood:	n/a	n/a
14	TAF1	chr12:31742550-31743150	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:31742631-31744748	GM19099	blood:	n/a	n/a
16	RAD21	chr12:31742666-31743145	SK-N-SH_RA	brain:	n/a	chr12:31743088-31743100 chr12:31743088-31743098
17	EP300	chr12:31742488-31744023	ECC-1	luminal epithelium:	n/a	chr12:31743322-31743338 chr12:31743067-31743083 chr12:31743295-31743311 chr12:31743015-31743031 chr12:31743063-31743079
18	CREB1	chr12:31742487-31743280	HepG2	liver:	n/a	n/a
19	NFIC	chr12:31742545-31743400	ECC-1	luminal epithelium:	n/a	n/a
20	TEAD4	chr12:31742593-31743150	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:31742561-31743173	HCT-116	colon:	n/a	n/a
22	POLR2A	chr12:31742665-31744720	GM18951	blood:	n/a	n/a
23	POLR2A	chr12:31742499-31743328	PANC-1	pancreas:	n/a	n/a
24	FOXA1	chr12:31742636-31743600	HepG2	liver:	n/a	n/a
25	POLR2A	chr12:31742612-31743417	HCT-116	colon:	n/a	n/a
26	RAD21	chr12:31742415-31743339	A549	lung:	n/a	chr12:31743088-31743100 chr12:31743088-31743098
27	POLR2A	chr12:31742560-31743362	GM12892	blood:	n/a	n/a
28	BHLHE40	chr12:31742555-31744782	HepG2	liver:	n/a	chr12:31743218-31743231 chr12:31743220-31743229 chr12:31743219-31743228 chr12:31743220-31743229 chr12:31744029-31744045
29	MAX	chr12:31742557-31743775	ECC-1	luminal epithelium:	n/a	n/a
30	ZBTB7A	chr12:31742587-31744501	ECC-1	luminal epithelium:	n/a	chr12:31743435-31743446
31	MAFK	chr12:31742518-31743199	Hela-S3	cervix:	n/a	n/a
32	SMC3	chr12:31742523-31743734	Hela-S3	cervix:	n/a	chr12:31743079-31743089
33	CTCF	chr12:31742560-31742710	GM06990	blood:	n/a	n/a
34	MAX	chr12:31742646-31744311	ECC-1	luminal epithelium:	n/a	chr12:31744239-31744248
35	MYC	chr12:31742601-31743704	NB4	blood:	n/a	n/a
36	MAX	chr12:31742522-31744059	A549	lung:	n/a	n/a
37	SMARCB1	chr12:31742650-31744448	Hela-S3	cervix:	n/a	chr12:31743311-31743320 chr12:31743310-31743319
38	EP300	chr12:31742575-31744313	SK-N-SH	brain:	n/a	chr12:31744263-31744279 chr12:31743322-31743338 chr12:31743067-31743083 chr12:31743295-31743311 chr12:31743015-31743031 chr12:31743063-31743079
39	ZNF217	chr12:31742615-31742923	MCF-7	breast:	n/a	n/a
40	POLR2A	chr12:31742476-31744109	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr12:31742634-31743280	HepG2	liver:	n/a	n/a
42	YY1	chr12:31742675-31742945	H1-hESC	embryonic stem cell:	n/a	chr12:31742789-31742800
43	SIN3AK20	chr12:31742522-31744401	PANC-1	pancreas:	n/a	n/a
44	RAD21	chr12:31742542-31743071	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr12:31742639-31744382	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:31742662-31744388	HUVEC	blood vessel:	n/a	n/a
47	SIN3A	chr12:31742569-31744603	H1-hESC	embryonic stem cell:	n/a	chr12:31743414-31743423 chr12:31743535-31743544 chr12:31742843-31742856 chr12:31743521-31743532
48	TCF12	chr12:31742559-31743309	ECC-1	luminal epithelium:	n/a	n/a
49	RAD21	chr12:31742604-31743974	H1-hESC	embryonic stem cell:	n/a	chr12:31743088-31743100 chr12:31743412-31743426 chr12:31743088-31743098
50	RUNX3	chr12:31742495-31744863	GM12878	blood:	n/a	chr12:31743445-31743462

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:31742648-31742698	AG10803	skin:	n/a
2	chr12:31742648-31742698	GM12892	blood:	n/a
3	chr12:31742648-31742698	HCF	heart:	n/a
4	chr12:31742648-31742698	NH-A	brain:	n/a
5	chr12:31742648-31742698	AG04449	skin:	fetal
6	chr12:31742648-31742698	SAEC	small airway:	n/a
7	chr12:31742648-31742698	NHBE	bronchial:	n/a
8	chr12:31742648-31742698	HCT-116	colon:	n/a
9	chr12:31742648-31742698	MCF-7	breast:	n/a
10	chr12:31742648-31742698	GM19239	blood:	n/a
11	chr12:31742648-31742698	HPAEpiC	pulmonary alveolar:	n/a
12	chr12:31742648-31742698	HEEpiC	esophagus:	n/a
13	chr12:31742648-31742698	H1-hESC	embryonic stem cell:	embryo
14	chr12:31742648-31742698	GM12891	blood:	n/a
15	chr12:31742648-31742698	T-47D	breast:	n/a
16	chr12:31742648-31742698	HIPEpiC	eye:	n/a
17	chr12:31742648-31742698	HAEpiC	amniotic membrane:	n/a
18	chr12:31742648-31742698	Jurkat	blood:	n/a
19	chr12:31742648-31742698	HRE	kidney:	n/a
20	chr12:31742648-31742698	AG09319	gingival:	n/a
21	chr12:31742648-31742698	NT2-D1	testis:	n/a
22	chr12:31742648-31742698	SK-N-MC	brain:	n/a
23	chr12:31742648-31742698	SKMC	muscle:	n/a
24	chr12:31742648-31742698	HCM	heart:	n/a
25	chr12:31742648-31742698	ECC-1	luminal epithelium:	n/a
26	chr12:31742648-31742698	ovcar-3	ovarian:	n/a
27	chr12:31742648-31742698	GM06990	blood:	n/a
28	chr12:31742648-31742698	HUVEC	blood vessel:	n/a
29	chr12:31742648-31742698	AoSMC	blood vessel:	n/a
30	chr12:31742648-31742698	Hepatocyte	liver:	n/a
31	chr12:31742648-31742698	AG04450	lung:	fetal
32	chr12:31742648-31742698	AG09309	skin:	n/a
33	chr12:31742648-31742698	HRCEpiC	kidney:	n/a
34	chr12:31742648-31742698	MCF10A-Er-Src	breast:	n/a
35	chr12:31742648-31742698	BJ	skin:	n/a
36	chr12:31742648-31742698	RPTEC	kidney:	n/a
37	chr12:31742648-31742698	PANC-1	pancreas:	n/a
38	chr12:31742648-31742698	A549	lung:	n/a
39	chr12:31742648-31742698	HCPEpiC	choroid plexus:	n/a
40	chr12:31742648-31742698	SK-N-SH	brain:	n/a
41	chr12:31742648-31742698	PrEC	prostate:	n/a
42	chr12:31742648-31742698	HepG2	liver:	n/a
43	chr12:31742648-31742698	NB4	blood:	n/a
44	chr12:31742648-31742698	BE2_C	brain:	n/a
45	chr12:31742648-31742698	IMR90	lung:	fetal
46	chr12:31742648-31742698	HNPCEpiC	eye:	n/a
47	chr12:31742648-31742698	LNCaP	prostate:	n/a
48	chr12:31742648-31742698	CMK	blood:	n/a
49	chr12:31742648-31742698	HRPEpiC	eye:	n/a
50	chr12:31742648-31742698	NHDF-neo	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31741307..31745552-chr12:31748528..31751513,3	MCF-7	breast:
2	chr12:31477472..31480749-chr12:31741860..31744200,4	MCF-7	breast:
3	chr12:31645308..31649621-chr12:31742506..31745309,6	MCF-7	breast:
4	chr12:31740792..31743101-chr12:31745770..31747885,3	MCF-7	breast:

Variant related genes	Relation type
DENND5B-AS1	TF binding region
DENND5B-AS1	CpG island
ENSG00000139146	Chromatin interaction
ENSG00000252390	Chromatin interaction
ENSG00000231788	Chromatin interaction
ENSG00000170456	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv1797962	chr12:31733044-31761172	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv3371967	chr12:31741685-31745983	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv558088	chr12:31742463-31743879	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv558089	chr12:31742463-31744089	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31741400-31745000	Active TSS	Ovary	ovary
2	chr12:31741600-31744200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr12:31741600-31744800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:31741600-31745000	Active TSS	Fetal Kidney	kidney
5	chr12:31741800-31742800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:31741800-31742800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:31741800-31743000	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr12:31741800-31743600	Active TSS	Right Atrium	heart
9	chr12:31741800-31744400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:31741800-31744400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr12:31741800-31744400	Active TSS	GM12878-XiMat	blood
12	chr12:31741800-31744800	Active TSS	Brain Cingulate Gyrus	brain
13	chr12:31741800-31745000	Active TSS	Rectal Smooth Muscle	rectum
14	chr12:31742000-31742800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:31742000-31742800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:31742000-31742800	Flanking Active TSS	NH-A	brain
17	chr12:31742000-31744200	Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr12:31742000-31744200	Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr12:31742000-31744400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:31742000-31744400	Active TSS	Fetal Intestine Small	intestine
21	chr12:31742000-31744400	Active TSS	HSMM	muscle
22	chr12:31742000-31744400	Active TSS	HSMMtube	muscle
23	chr12:31742000-31744600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:31742000-31744600	Active TSS	Brain Anterior Caudate	brain
25	chr12:31742000-31744600	Active TSS	Brain Germinal Matrix	brain
26	chr12:31742000-31744600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:31742000-31744600	Active TSS	Fetal Intestine Large	intestine
28	chr12:31742000-31744800	Active TSS	NHDF-Ad	bronchial
29	chr12:31742000-31745000	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr12:31742000-31745000	Active TSS	Right Ventricle	heart
31	chr12:31742200-31742800	Active TSS	H1 Cell Line	embryonic stem cell
32	chr12:31742200-31742800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr12:31742200-31742800	Active TSS	Primary T cells from cord blood	blood
34	chr12:31742200-31742800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr12:31742200-31743200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:31742200-31743200	Active TSS	Fetal Heart	heart
37	chr12:31742200-31744200	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr12:31742200-31744200	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr12:31742200-31744200	Active TSS	NHLF	lung
40	chr12:31742200-31744400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:31742200-31744400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:31742200-31744400	Active TSS	Brain Angular Gyrus	brain
43	chr12:31742200-31744400	Active TSS	Brain Hippocampus Middle	brain
44	chr12:31742200-31744400	Active TSS	Duodenum Mucosa	Duodenum
45	chr12:31742200-31744400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr12:31742200-31744400	Active TSS	HepG2	liver
47	chr12:31742200-31744600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr12:31742200-31744600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:31742200-31744800	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr12:31742200-31744800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links