Variant report

Variant	rs56061261
Chromosome Location	chr1:212606261-212606262
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	MAX	chr1:212605937-212606923	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:212605608-212606900	MCF10A-Er-Src	breast:	n/a	n/a
3	EGR1	chr1:212606026-212607203	K562	blood:	n/a	chr1:212606806-212606828 chr1:212607090-212607101 chr1:212607086-212607100 chr1:212607090-212607100 chr1:212607088-212607102 chr1:212607090-212607100 chr1:212606465-212606479 chr1:212606241-212606251 chr1:212607089-212607102 chr1:212607088-212607103 chr1:212607089-212607102 chr1:212607100-212607111 chr1:212606467-212606476
4	POLR2A	chr1:212606065-212606502	MCF-7	breast:	n/a	n/a
5	MYC	chr1:212605670-212606290	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:212605803-212606631	Hela-S3	cervix:	n/a	n/a
7	REST	chr1:212605928-212606650	K562	blood:	n/a	chr1:212606119-212606132
8	POLR2A	chr1:212605906-212606810	Hela-S3	cervix:	n/a	n/a
9	REST	chr1:212606146-212606487	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:212605709-212606498	K562	blood:	n/a	n/a
11	MAX	chr1:212605890-212606455	ECC-1	luminal epithelium:	n/a	n/a
12	REST	chr1:212606143-212606401	SK-N-SH	brain:	n/a	n/a
13	MAX	chr1:212605550-212607019	A549	lung:	n/a	n/a
14	BHLHE40	chr1:212605658-212606293	K562	blood:	n/a	n/a
15	POLR2A	chr1:212605931-212606273	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:212605671-212606482	K562	blood:	n/a	n/a
17	MAX	chr1:212605935-212606300	ECC-1	luminal epithelium:	n/a	n/a
18	IRF1	chr1:212605728-212606404	K562	blood:	n/a	chr1:212605917-212605929
19	CBX3	chr1:212605512-212606312	K562	blood:	n/a	n/a
20	POLR2A	chr1:212605919-212606489	NB4	blood:	n/a	n/a
21	POLR2A	chr1:212605643-212606458	GM12891	blood:	n/a	n/a
22	POLR2A	chr1:212605921-212606511	HepG2	liver:	n/a	n/a
23	HA-E2F1	chr1:212605844-212606723	MCF-7	breast:	n/a	chr1:212606197-212606212 chr1:212606242-212606251
24	MAX	chr1:212605981-212606518	K562	blood:	n/a	n/a
25	POLR2A	chr1:212605920-212606518	GM15510	blood:	n/a	n/a
26	POLR2A	chr1:212606061-212606502	MCF-7	breast:	n/a	n/a
27	POLR2A	chr1:212605902-212606541	Hela-S3	cervix:	n/a	n/a
28	YY1	chr1:212605997-212606735	K562	blood:	n/a	chr1:212606242-212606251 chr1:212606531-212606545
29	CEBPD	chr1:212606044-212606405	HepG2	liver:	n/a	n/a
30	TBL1XR1	chr1:212605721-212606608	K562	blood:	n/a	n/a
31	TCF12	chr1:212606022-212606305	GM12878	blood:	n/a	n/a
32	CHD2	chr1:212605820-212606352	GM12878	blood:	n/a	chr1:212606199-212606209
33	TBP	chr1:212605850-212606659	K562	blood:	n/a	n/a
34	MAZ	chr1:212605667-212606928	K562	blood:	n/a	n/a
35	REST	chr1:212605988-212606560	HepG2	liver:	n/a	chr1:212606119-212606132
36	POLR2A	chr1:212605712-212606530	K562	blood:	n/a	n/a
37	MAX	chr1:212605897-212606934	K562	blood:	n/a	n/a
38	MAX	chr1:212606071-212606271	H1-hESC	embryonic stem cell:	n/a	n/a
39	MYC	chr1:212605683-212606798	K562	blood:	n/a	n/a
40	FOXP2	chr1:212606028-212606313	SK-N-MC	brain:	n/a	n/a
41	REST	chr1:212606050-212606551	U87	brain:	n/a	chr1:212606119-212606132
42	HDAC2	chr1:212606014-212606468	K562	blood:	n/a	n/a
43	POLR2A	chr1:212605952-212606907	IMR90	lung:	n/a	n/a
44	TBP	chr1:212606241-212606330	HepG2	liver:	n/a	n/a
45	SMARCB1	chr1:212605973-212606990	Hela-S3	cervix:	n/a	n/a
46	IRF1	chr1:212605724-212606345	K562	blood:	n/a	chr1:212605917-212605929
47	TAF1	chr1:212606003-212606329	SK-N-SH	brain:	n/a	n/a
48	SIN3A	chr1:212606202-212606646	GM12878	blood:	n/a	n/a
49	REST	chr1:212606155-212606417	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr1:212605893-212606512	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212587912..212590110-chr1:212604889..212609190,4	K562	blood:
2	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
3	chr1:212604504..212608752-chr1:212780786..212783858,6	K562	blood:
4	chr1:212586060..212592297-chr1:212603893..212609565,9	MCF-7	breast:

Variant related genes	Relation type
NENF	TF binding region
ENSG00000162772	Chromatin interaction
ENSG00000065600	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	esv3389348	chr1:212605479-212607477	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212604600-212606400	Enhancers	Placenta Amnion	Placenta Amnion
2	chr1:212605600-212606600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:212605600-212606800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:212605600-212606800	Active TSS	Colon Smooth Muscle	Colon
5	chr1:212605600-212607000	Active TSS	Brain Hippocampus Middle	brain
6	chr1:212605600-212607000	Active TSS	Left Ventricle	heart
7	chr1:212605600-212607000	Active TSS	Ovary	ovary
8	chr1:212605600-212607000	Active TSS	Rectal Smooth Muscle	rectum
9	chr1:212605600-212607200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr1:212605600-212607200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:212605600-212607200	Active TSS	A549	lung
12	chr1:212605600-212607600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:212605600-212607600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr1:212605800-212606400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:212605800-212606600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr1:212605800-212606600	Active TSS	Fetal Brain Female	brain
17	chr1:212605800-212606800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:212605800-212606800	Active TSS	Liver	Liver
19	chr1:212605800-212606800	Active TSS	Brain Germinal Matrix	brain
20	chr1:212605800-212606800	Active TSS	Colonic Mucosa	Colon
21	chr1:212605800-212606800	Active TSS	Fetal Muscle Trunk	muscle
22	chr1:212605800-212606800	Active TSS	Fetal Muscle Leg	muscle
23	chr1:212605800-212606800	Active TSS	Fetal Thymus	thymus
24	chr1:212605800-212607000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr1:212605800-212607000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:212605800-212607000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:212605800-212607000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:212605800-212607000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:212605800-212607000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:212605800-212607000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:212605800-212607000	Active TSS	Psoas Muscle	Psoas
32	chr1:212605800-212607000	Active TSS	Right Atrium	heart
33	chr1:212605800-212607000	Active TSS	Right Ventricle	heart
34	chr1:212605800-212607000	Active TSS	HSMMtube	muscle
35	chr1:212605800-212607200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:212605800-212607200	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr1:212605800-212607200	Active TSS	NHDF-Ad	bronchial
38	chr1:212605800-212607200	Active TSS	NHLF	lung
39	chr1:212605800-212607400	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr1:212605800-212607400	Active TSS	Aorta	Aorta
41	chr1:212605800-212607400	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr1:212605800-212607400	Active TSS	Fetal Kidney	kidney
43	chr1:212605800-212607600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:212606000-212606400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:212606000-212606400	Active TSS	Primary B cells from cord blood	blood
46	chr1:212606000-212606400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:212606000-212606600	Active TSS	H1 Cell Line	embryonic stem cell
48	chr1:212606000-212606600	Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr1:212606000-212606600	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr1:212606000-212606800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links