Variant report

Variant	rs546779446
Chromosome Location	chr5:177557555-177557556
allele	C/G
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	ELF1	chr5:177557478-177559225	MCF-7	breast:	n/a	chr5:177558000-177558009 chr5:177557998-177558011 chr5:177557549-177557561 chr5:177558383-177558395 chr5:177557989-177558001 chr5:177558246-177558258
2	TBP	chr5:177557410-177558532	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:177557382-177558523	K562	blood:	n/a	n/a
4	POLR2A	chr5:177557420-177558452	A549	lung:	n/a	n/a
5	FOXM1	chr5:177557464-177558112	GM12878	blood:	n/a	n/a
6	ZBTB7A	chr5:177557399-177558087	K562	blood:	n/a	chr5:177557818-177557829
7	TAF7	chr5:177557398-177558515	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr5:177557474-177557938	K562	blood:	n/a	n/a
9	TAF1	chr5:177557546-177558335	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr5:177557295-177558393	HUVEC	blood vessel:	n/a	n/a
11	RFX5	chr5:177557461-177558007	HepG2	liver:	n/a	chr5:177557795-177557811 chr5:177557485-177557498
12	POLR2A	chr5:177557457-177558182	HepG2	liver:	n/a	n/a
13	POLR2A	chr5:177557524-177558240	Gliobla	brain:	n/a	n/a
14	MAX	chr5:177557520-177558270	HCT-116	colon:	n/a	n/a
15	POLR2A	chr5:177557524-177558414	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr5:177557385-177558239	A549	lung:	n/a	n/a
17	POLR2A	chr5:177557315-177559003	GM12891	blood:	n/a	n/a
18	MAZ	chr5:177557360-177558575	IMR90	lung:	n/a	n/a
19	RCOR1	chr5:177557284-177558807	K562	blood:	n/a	n/a
20	SMC3	chr5:177557484-177558372	Hela-S3	cervix:	n/a	n/a
21	GABPA	chr5:177557501-177558345	SK-N-SH	brain:	n/a	chr5:177558126-177558135
22	POLR2A	chr5:177557246-177558921	SK-N-MC	brain:	n/a	n/a
23	UBTF	chr5:177557418-177558414	K562	blood:	n/a	n/a
24	TAF1	chr5:177557263-177558617	H1-hESC	embryonic stem cell:	n/a	n/a
25	SIN3A	chr5:177557522-177558878	H1-hESC	embryonic stem cell:	n/a	chr5:177558252-177558261 chr5:177558281-177558294 chr5:177558481-177558494 chr5:177558099-177558112
26	CHD1	chr5:177557357-177558395	H1-hESC	embryonic stem cell:	n/a	n/a
27	EBF1	chr5:177557462-177558083	GM12878	blood:	n/a	n/a
28	MAX	chr5:177557496-177558165	SK-N-SH	brain:	n/a	n/a
29	GABPA	chr5:177557503-177558443	A549	lung:	n/a	chr5:177558126-177558135
30	PML	chr5:177557510-177558289	K562	blood:	n/a	n/a
31	SRF	chr5:177557509-177558262	MCF-7	breast:	n/a	n/a
32	CTCF	chr5:177557540-177557690	SAEC	small airway:	n/a	n/a
33	GATA3	chr5:177557355-177558372	MCF-7	breast:	n/a	n/a
34	CTCF	chr5:177557500-177557650	AG09319	gingival:	n/a	n/a
35	POLR2A	chr5:177557180-177559198	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr5:177557360-177558449	HCT-116	colon:	n/a	n/a
37	IRF1	chr5:177557515-177558461	K562	blood:	n/a	chr5:177557965-177557979
38	POLR2A	chr5:177557418-177558529	GM19193	blood:	n/a	n/a
39	TAF1	chr5:177557396-177558397	K562	blood:	n/a	n/a
40	HDAC2	chr5:177557467-177558476	MCF-7	breast:	n/a	n/a
41	JUND	chr5:177557485-177558186	H1-hESC	embryonic stem cell:	n/a	chr5:177557720-177557729
42	SIN3AK20	chr5:177557479-177558397	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr5:177557260-177558064	U87	brain:	n/a	n/a
44	POLR2A	chr5:177557432-177558258	HepG2	liver:	n/a	n/a
45	POLR2A	chr5:177557420-177558211	HepG2	liver:	n/a	n/a
46	SIN3AK20	chr5:177557328-177558563	SK-N-SH	brain:	n/a	n/a
47	HMGN3	chr5:177557452-177558418	K562	blood:	n/a	n/a
48	ZMIZ1	chr5:177557475-177558278	K562	blood:	n/a	n/a
49	POLR2A	chr5:177557264-177558400	PANC-1	pancreas:	n/a	n/a
50	ZC3H11A	chr5:177557484-177558176	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:177556499..177561085-chr5:177629309..177633856,7	K562	blood:
2	chr5:177557386..177557994-chr7:96162492..96163492,2	HCT-116	colon:
3	chr11:62608645..62609556-chr5:177557343..177558256,2	NB4	blood:
4	chr5:177556214..177559808-chr5:177575521..177582645,10	K562	blood:
5	chr5:177556514..177559685-chr5:177630098..177633052,4	K562	blood:
6	chr5:177554586..177557949-chr5:177561501..177564806,6	K562	blood:
7	chr5:177556060..177559207-chr5:177571980..177574313,5	K562	blood:
8	chr1:28240140..28241106-chr5:177557176..177557955,2	Hela-S3	cervix:
9	chr5:177556060..177559089-chr5:177572421..177574313,3	K562	blood:
10	chr5:177556823..177560281-chr5:177564764..177567288,3	K562	blood:
11	chr5:177556550..177559096-chr5:177579482..177582645,4	K562	blood:
12	chr5:177555803..177560183-chr5:177628551..177633825,8	MCF-7	breast:

Variant related genes	Relation type
RMND5B	TF binding region
ENSG00000117748	Chromatin interaction
ENSG00000145916	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000145912	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
3	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
5	nsv462567	chr5:177505021-177572927	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
6	nsv471058	chr5:177505021-177572927	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv600392	chr5:177505021-177572927	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
9	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv883192	chr5:177535370-177564346	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv600394	chr5:177549491-177608195	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	esv3424416	chr5:177556571-177559319	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr5:177549400-177558200	Weak transcription	Fetal Heart	heart
2	chr5:177556800-177558600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:177556800-177559600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:177557000-177557800	Enhancers	Fetal Brain Male	brain
5	chr5:177557000-177558600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr5:177557000-177558600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:177557000-177558600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr5:177557000-177558600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:177557000-177558600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:177557000-177558600	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr5:177557000-177558600	Active TSS	Stomach Smooth Muscle	stomach
12	chr5:177557000-177558600	Bivalent/Poised TSS	HepG2	liver
13	chr5:177557000-177558800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:177557000-177559000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:177557200-177557600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr5:177557200-177557600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr5:177557200-177557600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr5:177557200-177557600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:177557200-177557600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr5:177557200-177557600	Flanking Active TSS	Fetal Thymus	thymus
21	chr5:177557200-177557600	Active TSS	Right Atrium	heart
22	chr5:177557200-177557600	Flanking Active TSS	Dnd41	blood
23	chr5:177557200-177557800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr5:177557200-177557800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:177557200-177557800	Flanking Active TSS	HUVEC	blood vessel
26	chr5:177557200-177558200	Active TSS	Monocytes-CD14+_RO01746	blood
27	chr5:177557200-177558400	Active TSS	Primary T cells from cord blood	blood
28	chr5:177557200-177558400	Active TSS	Fetal Muscle Trunk	muscle
29	chr5:177557200-177558600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:177557200-177558600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:177557200-177558600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:177557200-177558600	Active TSS	Brain Angular Gyrus	brain
33	chr5:177557200-177558600	Active TSS	Brain Anterior Caudate	brain
34	chr5:177557200-177558600	Active TSS	Brain Cingulate Gyrus	brain
35	chr5:177557200-177558600	Active TSS	Brain Germinal Matrix	brain
36	chr5:177557200-177558600	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr5:177557200-177558600	Active TSS	Brain Substantia Nigra	brain
38	chr5:177557200-177558600	Active TSS	Colon Smooth Muscle	Colon
39	chr5:177557200-177558600	Active TSS	Duodenum Mucosa	Duodenum
40	chr5:177557200-177558600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr5:177557200-177558600	Active TSS	Fetal Brain Female	brain
42	chr5:177557200-177558600	Active TSS	Fetal Intestine Large	intestine
43	chr5:177557200-177558600	Active TSS	Placenta	Placenta
44	chr5:177557200-177558600	Active TSS	Ovary	ovary
45	chr5:177557200-177558600	Active TSS	Placenta Amnion	Placenta Amnion
46	chr5:177557200-177558600	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr5:177557200-177558600	Active TSS	Rectal Smooth Muscle	rectum
48	chr5:177557200-177558600	Active TSS	Thymus	Thymus
49	chr5:177557200-177558600	Active TSS	GM12878-XiMat	blood
50	chr5:177557200-177558600	Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links