Variant report

Variant	rs546040457
Chromosome Location	chr2:48570900-48570901
allele	-/A
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	TCF7L2	chr2:48570898-48571786	PANC-1	pancreas:	n/a	chr2:48571404-48571420 chr2:48571405-48571419 chr2:48571404-48571420
2	KAP1	chr2:48570881-48571860	HEK293	kidney:	n/a	chr2:48571522-48571531
3	MYBL2	chr2:48570798-48571818	HepG2	liver:	n/a	chr2:48571399-48571412
4	TCF12	chr2:48570813-48571987	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr2:48570574-48572155	A549	lung:	n/a	n/a
6	GATA3	chr2:48570616-48572011	SK-N-SH	brain:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
7	KAP1	chr2:48570845-48571789	U2OS	brain:	n/a	chr2:48571522-48571531
8	ZNF384	chr2:48570751-48571103	K562	blood:	n/a	n/a
9	GATA3	chr2:48570698-48571959	SK-N-SH	brain:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
10	POLR2A	chr2:48570735-48571779	U87	brain:	n/a	n/a
11	FOXA2	chr2:48570899-48573824	HepG2	liver:	n/a	chr2:48571194-48571206 chr2:48571350-48571362
12	SP1	chr2:48570675-48571831	A549	lung:	n/a	n/a
13	GATA1	chr2:48570703-48571703	PBDE	blood:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
14	TCF7L2	chr2:48570851-48571713	Hela-S3	cervix:	n/a	chr2:48571404-48571420 chr2:48571405-48571419 chr2:48571404-48571420
15	SETDB1	chr2:48570771-48571721	U2OS	brain:	n/a	n/a
16	FOXA1	chr2:48570844-48571796	A549	lung:	n/a	chr2:48571194-48571206 chr2:48571350-48571362
17	TCF12	chr2:48570853-48571944	SK-N-SH	brain:	n/a	n/a
18	GATA3	chr2:48570808-48571971	A549	lung:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
19	BCL3	chr2:48570810-48571714	A549	lung:	n/a	n/a
20	FOXA1	chr2:48570889-48571767	A549	lung:	n/a	chr2:48571194-48571206 chr2:48571350-48571362
21	MAX	chr2:48570658-48571266	A549	lung:	n/a	n/a
22	EP300	chr2:48570712-48571809	A549	lung:	n/a	chr2:48571121-48571135
23	CEBPB	chr2:48570855-48571744	Hela-S3	cervix:	n/a	n/a
24	EP300	chr2:48570750-48571850	A549	lung:	n/a	chr2:48571121-48571135
25	PBX3	chr2:48570883-48571928	SK-N-SH	brain:	n/a	n/a
26	ZNF384	chr2:48570841-48571149	GM12878	blood:	n/a	n/a
27	GATA2	chr2:48570719-48571746	HUVEC	blood vessel:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571465-48571479 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
28	RFX5	chr2:48570866-48571774	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr2:48570741-48571773	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:48337910..48340125-chr2:48569442..48571000,2	MCF-7	breast:
2	chr2:48568928..48571039-chr2:48579815..48581773,2	MCF-7	breast:
3	chr2:48541369..48544104-chr2:48569607..48573166,3	MCF-7	breast:

Variant related genes	Relation type
RNU4-49P	TF binding region
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48553400-48574400	Weak transcription	Lung	lung
2	chr2:48556800-48571600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:48557000-48573200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:48557000-48573400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:48558400-48571400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:48558800-48571200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:48559800-48573400	Weak transcription	Fetal Kidney	kidney
8	chr2:48559800-48573400	Weak transcription	Right Atrium	heart
9	chr2:48560600-48573600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:48561000-48571200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:48561600-48571400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:48561800-48571000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:48562000-48573400	Weak transcription	Psoas Muscle	Psoas
14	chr2:48562000-48573400	Weak transcription	K562	blood
15	chr2:48562200-48571000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:48564800-48574400	Weak transcription	Fetal Stomach	stomach
17	chr2:48565800-48571800	Weak transcription	Fetal Intestine Small	intestine
18	chr2:48566600-48573600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:48566800-48571000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:48567200-48571400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:48567400-48571000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:48567400-48571000	Enhancers	Brain Substantia Nigra	brain
23	chr2:48568800-48571000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:48569000-48571000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:48569000-48571000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:48569000-48571000	Weak transcription	HSMMtube	muscle
27	chr2:48569000-48571200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:48569000-48573400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:48569000-48573400	Weak transcription	Brain Germinal Matrix	brain
30	chr2:48569000-48573400	Weak transcription	Fetal Lung	lung
31	chr2:48569000-48573400	Weak transcription	Pancreas	Pancrea
32	chr2:48569000-48574400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:48569000-48580000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:48569200-48571000	Enhancers	Brain Angular Gyrus	brain
35	chr2:48569200-48571000	Enhancers	Brain Hippocampus Middle	brain
36	chr2:48569200-48573400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:48569400-48571000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:48569600-48571000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr2:48569800-48571000	Enhancers	Liver	Liver
40	chr2:48569800-48571000	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr2:48570000-48571000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr2:48570000-48571000	Enhancers	Dnd41	blood
43	chr2:48570200-48571000	Enhancers	Primary T cells from cord blood	blood
44	chr2:48570200-48572600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr2:48570400-48571000	Flanking Active TSS	A549	lung
46	chr2:48570400-48571000	Enhancers	NHEK	skin
47	chr2:48570400-48571200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:48570600-48571000	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr2:48570600-48571000	Enhancers	Primary hematopoietic stem cells	blood
50	chr2:48570600-48571000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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