Variant report

Variant	rs554762749
Chromosome Location	chr1:224622922-224622923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:287)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:287 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr1:224622879-224622967	Hela-S3	cervix:	n/a	n/a
2	USF1	chr1:224622361-224622938	K562	blood:	n/a	n/a
3	MAX	chr1:224622382-224623283	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:224620773-224622966	H1-neurons	neurons:	n/a	n/a
5	KAP1	chr1:224622625-224623298	HEK293	kidney:	n/a	n/a
6	YY1	chr1:224622361-224623096	ECC-1	luminal epithelium:	n/a	chr1:224622898-224622909
7	MAX	chr1:224622386-224623011	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:224622145-224623102	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:224622192-224623088	MCF-7	breast:	n/a	n/a
10	MAX	chr1:224622368-224623475	K562	blood:	n/a	n/a
11	POLR2A	chr1:224622296-224623507	K562	blood:	n/a	n/a
12	POLR2A	chr1:224621186-224623237	GM19193	blood:	n/a	n/a
13	POLR2A	chr1:224621161-224623458	Raji	blood:	n/a	n/a
14	GABPA	chr1:224622259-224623068	A549	lung:	n/a	n/a
15	POLR2A	chr1:224622333-224623541	K562	blood:	n/a	n/a
16	POLR2A	chr1:224622267-224622957	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:224622280-224624163	MCF10A-Er-Src	breast:	n/a	n/a
18	CEBPB	chr1:224622423-224623586	K562	blood:	n/a	chr1:224622987-224622998
19	YY1	chr1:224622363-224623032	ECC-1	luminal epithelium:	n/a	chr1:224622898-224622909
20	POLR2A	chr1:224622197-224623322	GM12891	blood:	n/a	n/a
21	TCF12	chr1:224622357-224623355	ECC-1	luminal epithelium:	n/a	n/a
22	RUNX3	chr1:224622363-224623329	GM12878	blood:	n/a	n/a
23	ZBTB7A	chr1:224622084-224623116	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr1:224621852-224623553	K562	blood:	n/a	n/a
25	GABPA	chr1:224622194-224623124	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:224619112-224623610	IMR90	lung:	n/a	n/a
27	POLR2A	chr1:224622269-224623349	GM12878	blood:	n/a	n/a
28	CBX3	chr1:224622348-224623594	K562	blood:	n/a	n/a
29	GTF2F1	chr1:224622388-224623439	Hela-S3	cervix:	n/a	n/a
30	MYC	chr1:224622379-224623426	K562	blood:	n/a	n/a
31	POLR2A	chr1:224622264-224622969	GM12892	blood:	n/a	n/a
32	POLR2A	chr1:224621383-224623145	MCF-7	breast:	n/a	n/a
33	CREB1	chr1:224622248-224623666	K562	blood:	n/a	n/a
34	MAZ	chr1:224622430-224622970	Hela-S3	cervix:	n/a	n/a
35	MAX	chr1:224622383-224623131	MCF-7	breast:	n/a	n/a
36	TRIM28	chr1:224622332-224623552	K562	blood:	n/a	n/a
37	TBL1XR1	chr1:224622555-224623351	K562	blood:	n/a	n/a
38	POLR2A	chr1:224622300-224622934	A549	lung:	n/a	n/a
39	ZC3H11A	chr1:224622418-224623357	K562	blood:	n/a	n/a
40	MXI1	chr1:224622177-224624682	SK-N-SH	brain:	n/a	n/a
41	TAF1	chr1:224622321-224622980	A549	lung:	n/a	n/a
42	UBTF	chr1:224621421-224623388	K562	blood:	n/a	n/a
43	MXI1	chr1:224622395-224623496	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr1:224622350-224622966	SK-N-MC	brain:	n/a	n/a
45	POLR2A	chr1:224622243-224623190	GM12891	blood:	n/a	n/a
46	POLR2A	chr1:224621499-224623220	GM12878	blood:	n/a	n/a
47	SIN3AK20	chr1:224622333-224622923	SK-N-SH	brain:	n/a	n/a
48	RCOR1	chr1:224622425-224623543	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr1:224622389-224623646	PBDE	blood:	n/a	n/a
50	ETS1	chr1:224622262-224623135	K562	blood:	n/a	chr1:224622274-224622285

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:224621434..224624086-chr12:120727815..120730107,2	MCF-7	breast:
2	chr1:224595603..224601847-chr1:224621020..224623770,7	MCF-7	breast:
3	chr1:224544325..224548164-chr1:224620481..224623704,4	K562	blood:
4	chr1:224543329..224547108-chr1:224619239..224622996,5	MCF-7	breast:
5	chr1:224586518..224588836-chr1:224621196..224623489,2	MCF-7	breast:
6	chr1:224585388..224587684-chr1:224620366..224622924,3	K562	blood:
7	chr1:224301465..224303000-chr1:224620703..224623446,2	K562	blood:

No data

Variant related genes	Relation type
WDR26	TF binding region
ENSG00000162923	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000266618	Chromatin interaction
ENSG00000143771	Chromatin interaction
ENSG00000143756	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1013149	chr1:224605943-224646382	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv535312	chr1:224605943-224646382	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3422629	chr1:224620954-224623702	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv3353372	chr1:224621279-224623577	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr1:224618400-224623400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:224618400-224623400	Active TSS	Right Atrium	heart
3	chr1:224618400-224623600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:224618600-224623400	Active TSS	Aorta	Aorta
5	chr1:224618800-224623000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:224619400-224623000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:224619400-224623200	Active TSS	Right Ventricle	heart
8	chr1:224619600-224623000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:224619600-224623000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:224619600-224623200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:224619600-224623200	Active TSS	Fetal Intestine Large	intestine
12	chr1:224619600-224623200	Active TSS	GM12878-XiMat	blood
13	chr1:224619600-224623200	Active TSS	HSMMtube	muscle
14	chr1:224619600-224623400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:224619600-224623800	Active TSS	Psoas Muscle	Psoas
16	chr1:224619800-224623000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:224619800-224623000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:224619800-224623000	Active TSS	Colon Smooth Muscle	Colon
19	chr1:224619800-224623000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:224619800-224623000	Active TSS	Fetal Thymus	thymus
21	chr1:224619800-224623200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr1:224619800-224623400	Active TSS	NHLF	lung
23	chr1:224619800-224623600	Active TSS	NHDF-Ad	bronchial
24	chr1:224620000-224623000	Active TSS	Muscle Satellite Cultured Cells	--
25	chr1:224620000-224623400	Active TSS	Ovary	ovary
26	chr1:224620000-224624000	Active TSS	Fetal Intestine Small	intestine
27	chr1:224620200-224623400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:224620400-224623000	Active TSS	Brain Substantia Nigra	brain
29	chr1:224620400-224623200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:224620400-224623200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr1:224620400-224623200	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr1:224620400-224623400	Active TSS	Esophagus	oesophagus
33	chr1:224620400-224623400	Active TSS	Fetal Kidney	kidney
34	chr1:224620400-224623400	Active TSS	Lung	lung
35	chr1:224620600-224623000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:224620600-224623000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:224620600-224623000	Active TSS	Brain Angular Gyrus	brain
38	chr1:224620600-224623000	Active TSS	HSMM	muscle
39	chr1:224620600-224623400	Active TSS	Gastric	stomach
40	chr1:224620800-224623000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:224620800-224623000	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr1:224620800-224623000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr1:224620800-224623200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:224620800-224623200	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr1:224620800-224623200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr1:224620800-224623400	Active TSS	Small Intestine	intestine
47	chr1:224621000-224623000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:224621000-224623000	Active TSS	Primary T cells from cord blood	blood
49	chr1:224621000-224623000	Active TSS	Brain Hippocampus Middle	brain
50	chr1:224621000-224623000	Active TSS	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links