Variant report

Variant	rs562484243
Chromosome Location	chr12:31743774-31743775
allele	G/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	POLR2A	chr12:31742728-31744436	Gliobla	brain:	n/a	n/a
2	POLR2A	chr12:31742347-31744772	IMR90	lung:	n/a	n/a
3	POLR2A	chr12:31742595-31744836	GM19193	blood:	n/a	n/a
4	POLR2A	chr12:31742731-31744254	ECC-1	luminal epithelium:	n/a	n/a
5	UBTF	chr12:31742865-31744130	K562	blood:	n/a	n/a
6	RCOR1	chr12:31743240-31744121	K562	blood:	n/a	n/a
7	POLR2A	chr12:31742607-31744526	HepG2	liver:	n/a	n/a
8	CREB1	chr12:31743274-31743810	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:31742606-31744703	NB4	blood:	n/a	n/a
10	TAF1	chr12:31743174-31744796	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr12:31742723-31744440	A549	lung:	n/a	n/a
12	POLR2A	chr12:31742804-31744113	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F1	chr12:31742985-31744369	Hela-S3	cervix:	n/a	chr12:31743079-31743089 chr12:31743564-31743573 chr12:31744163-31744172
14	TBP	chr12:31742788-31744007	K562	blood:	n/a	n/a
15	POLR2A	chr12:31742631-31744748	GM19099	blood:	n/a	n/a
16	YY1	chr12:31743648-31744354	GM12878	blood:	n/a	chr12:31744268-31744279 chr12:31744265-31744279
17	YY1	chr12:31743181-31744043	GM12878	blood:	n/a	chr12:31743295-31743309 chr12:31743243-31743257 chr12:31743435-31743449
18	YY1	chr12:31742997-31744118	K562	blood:	n/a	chr12:31743295-31743309 chr12:31743082-31743096 chr12:31743076-31743087 chr12:31743243-31743257 chr12:31743166-31743177 chr12:31743435-31743449
19	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
20	MAX	chr12:31742722-31744366	K562	blood:	n/a	chr12:31744239-31744248
21	POLR2A	chr12:31742665-31744720	GM18951	blood:	n/a	n/a
22	POLR2A	chr12:31743433-31744337	A549	lung:	n/a	n/a
23	POLR2A	chr12:31743770-31744365	Hela-S3	cervix:	n/a	n/a
24	BHLHE40	chr12:31742555-31744782	HepG2	liver:	n/a	chr12:31743218-31743231 chr12:31743220-31743229 chr12:31743219-31743228 chr12:31743220-31743229 chr12:31744029-31744045
25	POLR2A	chr12:31743738-31744154	HUVEC	blood vessel:	n/a	n/a
26	MAX	chr12:31742557-31743775	ECC-1	luminal epithelium:	n/a	n/a
27	ZBTB7A	chr12:31742587-31744501	ECC-1	luminal epithelium:	n/a	chr12:31743435-31743446
28	POLR2A	chr12:31743359-31743981	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:31742694-31744542	GM10847	blood:	n/a	n/a
30	MAX	chr12:31742646-31744311	ECC-1	luminal epithelium:	n/a	chr12:31744239-31744248
31	POLR2A	chr12:31742727-31744396	HepG2	liver:	n/a	n/a
32	POLR2A	chr12:31743476-31744345	A549	lung:	n/a	n/a
33	MAX	chr12:31742522-31744059	A549	lung:	n/a	n/a
34	GATA3	chr12:31743700-31745058	A549	lung:	n/a	chr12:31744727-31744736
35	SMARCB1	chr12:31742650-31744448	Hela-S3	cervix:	n/a	chr12:31743311-31743320 chr12:31743310-31743319
36	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
37	POLR2A	chr12:31743765-31744093	HepG2	liver:	n/a	n/a
38	MYC	chr12:31742926-31744300	K562	blood:	n/a	chr12:31744239-31744248
39	POLR2A	chr12:31742476-31744109	Hela-S3	cervix:	n/a	n/a
40	SIN3AK20	chr12:31742522-31744401	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr12:31742639-31744382	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:31742662-31744388	HUVEC	blood vessel:	n/a	n/a
43	SIN3A	chr12:31742569-31744603	H1-hESC	embryonic stem cell:	n/a	chr12:31743414-31743423 chr12:31743535-31743544 chr12:31742843-31742856 chr12:31743521-31743532
44	RAD21	chr12:31742604-31743974	H1-hESC	embryonic stem cell:	n/a	chr12:31743088-31743100 chr12:31743412-31743426 chr12:31743088-31743098
45	RUNX3	chr12:31742495-31744863	GM12878	blood:	n/a	chr12:31743445-31743462
46	TAF1	chr12:31743481-31744416	HepG2	liver:	n/a	n/a
47	POLR2A	chr12:31742652-31744833	HUVEC	blood vessel:	n/a	n/a
48	MAZ	chr12:31742647-31744591	Hela-S3	cervix:	n/a	chr12:31744239-31744248
49	TAF1	chr12:31743488-31744334	HepG2	liver:	n/a	n/a
50	POLR2A	chr12:31742574-31744772	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31741307..31745552-chr12:31748528..31751513,3	MCF-7	breast:
2	chr12:31477521..31479099-chr12:31743621..31745412,2	K562	blood:
3	chr12:31477472..31480749-chr12:31741860..31744200,4	MCF-7	breast:
4	chr12:31645308..31649621-chr12:31742506..31745309,6	MCF-7	breast:
5	chr12:31743215..31744081-chr19:1875675..1876438,2	Hela-S3	cervix:

Variant related genes	Relation type
DENND5B-AS1	TF binding region
DENND5B	TF binding region
ENSG00000170456	Chromatin interaction
ENSG00000231788	Chromatin interaction
ENSG00000139146	Chromatin interaction
ENSG00000261526	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:25 , 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
12	esv3375615	chr12:31742710-31745258	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv558090	chr12:31743194-31743825	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv558091	chr12:31743194-31743879	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	nsv558092	chr12:31743194-31744033	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	nsv558093	chr12:31743194-31744089	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
17	esv1804747	chr12:31743194-31748491	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	esv1840310	chr12:31743194-31750986	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	esv18875	chr12:31743202-31744209	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
20	nsv558094	chr12:31743319-31743936	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
21	nsv558095	chr12:31743319-31744089	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
22	nsv558096	chr12:31743365-31743936	Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
23	nsv558097	chr12:31743365-31744033	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
24	nsv558098	chr12:31743365-31744089	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
25	nsv558099	chr12:31743416-31744089	Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 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	chr12:31741400-31745000	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	chr12:31741800-31744400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:31741800-31744400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr12:31741800-31744400	Active TSS	GM12878-XiMat	blood
8	chr12:31741800-31744800	Active TSS	Brain Cingulate Gyrus	brain
9	chr12:31741800-31745000	Active TSS	Rectal Smooth Muscle	rectum
10	chr12:31742000-31744200	Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr12:31742000-31744200	Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr12:31742000-31744400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:31742000-31744400	Active TSS	Fetal Intestine Small	intestine
14	chr12:31742000-31744400	Active TSS	HSMM	muscle
15	chr12:31742000-31744400	Active TSS	HSMMtube	muscle
16	chr12:31742000-31744600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:31742000-31744600	Active TSS	Brain Anterior Caudate	brain
18	chr12:31742000-31744600	Active TSS	Brain Germinal Matrix	brain
19	chr12:31742000-31744600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:31742000-31744600	Active TSS	Fetal Intestine Large	intestine
21	chr12:31742000-31744800	Active TSS	NHDF-Ad	bronchial
22	chr12:31742000-31745000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:31742000-31745000	Active TSS	Right Ventricle	heart
24	chr12:31742200-31744200	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr12:31742200-31744200	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr12:31742200-31744200	Active TSS	NHLF	lung
27	chr12:31742200-31744400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:31742200-31744400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:31742200-31744400	Active TSS	Brain Angular Gyrus	brain
30	chr12:31742200-31744400	Active TSS	Brain Hippocampus Middle	brain
31	chr12:31742200-31744400	Active TSS	Duodenum Mucosa	Duodenum
32	chr12:31742200-31744400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr12:31742200-31744400	Active TSS	HepG2	liver
34	chr12:31742200-31744600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr12:31742200-31744600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:31742200-31744800	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr12:31742200-31744800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:31742200-31744800	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr12:31742200-31744800	Active TSS	NHEK	skin
40	chr12:31742200-31745000	Active TSS	Colon Smooth Muscle	Colon
41	chr12:31742200-31745000	Active TSS	Fetal Brain Female	brain
42	chr12:31742400-31744200	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr12:31742400-31744200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:31742400-31744200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:31742400-31744200	Active TSS	Fetal Muscle Trunk	muscle
46	chr12:31742400-31744200	Active TSS	Placenta	Placenta
47	chr12:31742400-31744200	Active TSS	HMEC	breast
48	chr12:31742400-31744400	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr12:31742400-31744400	Active TSS	Fetal Lung	lung
50	chr12:31742400-31744400	Active TSS	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links