Variant report

Variant	rs550272345
Chromosome Location	chr5:59996667-59996668
allele	A/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	POLR2A	chr5:59995284-59996921	K562	blood:	n/a	n/a
2	ATF1	chr5:59995447-59996702	K562	blood:	n/a	n/a
3	MYC	chr5:59995284-59996677	K562	blood:	n/a	n/a
4	POLR2A	chr5:59995227-59997036	SK-N-MC	brain:	n/a	n/a
5	HCFC1	chr5:59994863-59996773	Hela-S3	cervix:	n/a	n/a
6	MAX	chr5:59995202-59996774	HCT-116	colon:	n/a	n/a
7	CEBPB	chr5:59996231-59997044	K562	blood:	n/a	n/a
8	MTA3	chr5:59994872-59996687	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:59995318-59996812	HepG2	liver:	n/a	n/a
10	HA-E2F1	chr5:59995291-59996896	MCF-7	breast:	n/a	chr5:59996023-59996032
11	MYC	chr5:59995070-59997191	K562	blood:	n/a	n/a
12	E2F4	chr5:59994881-59997215	MCF10A-Er-Src	breast:	n/a	chr5:59996023-59996032
13	FOXM1	chr5:59995378-59996714	MCF-7	breast:	n/a	n/a
14	POLR2A	chr5:59994852-59996810	GM12878	blood:	n/a	n/a
15	BHLHE40	chr5:59995469-59997496	K562	blood:	n/a	chr5:59995940-59995956 chr5:59995931-59995947
16	E2F6	chr5:59995310-59996733	A549	lung:	n/a	chr5:59996023-59996032
17	JUND	chr5:59995155-59996866	K562	blood:	n/a	chr5:59995330-59995344 chr5:59996617-59996625
18	RELA	chr5:59995183-59996676	GM18951	blood:	n/a	n/a
19	MXI1	chr5:59994719-59997063	SK-N-SH	brain:	n/a	n/a
20	E2F6	chr5:59995328-59996721	H1-hESC	embryonic stem cell:	n/a	chr5:59996023-59996032
21	EBF1	chr5:59996439-59996801	GM12878	blood:	n/a	chr5:59996648-59996659 chr5:59996648-59996661
22	E2F6	chr5:59995333-59996783	K562	blood:	n/a	chr5:59996023-59996032
23	TCF12	chr5:59995160-59996732	A549	lung:	n/a	n/a
24	NR2F2	chr5:59995332-59996682	MCF-7	breast:	n/a	n/a
25	GABPA	chr5:59994991-59996701	MCF-7	breast:	n/a	n/a
26	POLR2A	chr5:59995082-59997876	H1-hESC	embryonic stem cell:	n/a	n/a
27	REST	chr5:59995188-59996720	H1-neurons	neurons:	n/a	chr5:59996092-59996105
28	MAX	chr5:59995157-59996700	HepG2	liver:	n/a	n/a
29	RCOR1	chr5:59994968-59996685	K562	blood:	n/a	n/a
30	CBX3	chr5:59995381-59996849	K562	blood:	n/a	n/a
31	UBTF	chr5:59994991-59996847	K562	blood:	n/a	n/a
32	CCNT2	chr5:59995634-59996720	K562	blood:	n/a	chr5:59996179-59996188
33	POLR2A	chr5:59995335-59996748	K562	blood:	n/a	n/a
34	MXI1	chr5:59994764-59997204	IMR90	lung:	n/a	n/a
35	POLR2A	chr5:59995356-59997148	K562	blood:	n/a	n/a
36	E2F6	chr5:59995320-59997021	H1-hESC	embryonic stem cell:	n/a	chr5:59996023-59996032
37	USF2	chr5:59996176-59996779	K562	blood:	n/a	n/a
38	SIN3AK20	chr5:59995082-59997103	MCF-7	breast:	n/a	n/a
39	POLR2A	chr5:59995354-59997661	K562	blood:	n/a	n/a
40	POLR2A	chr5:59995297-59996810	GM12891	blood:	n/a	n/a
41	CREB1	chr5:59995652-59996713	K562	blood:	n/a	n/a
42	MAX	chr5:59995280-59996718	A549	lung:	n/a	n/a
43	POLR2A	chr5:59995331-59996741	K562	blood:	n/a	n/a
44	CTCF	chr5:59995020-59997049	SK-N-SH	brain:	n/a	chr5:59995612-59995630 chr5:59995613-59995629 chr5:59995930-59995943 chr5:59995964-59995977
45	POLR2A	chr5:59995386-59997156	HepG2	liver:	n/a	n/a
46	ZNF263	chr5:59994888-59996687	HEK293-T-REx	kidney:	n/a	n/a
47	POLR2A	chr5:59995361-59997028	K562	blood:	n/a	n/a
48	GATA3	chr5:59995288-59996718	MCF-7	breast:	n/a	n/a
49	MAX	chr5:59995285-59996713	MCF-7	breast:	n/a	n/a
50	GATA1	chr5:59995405-59997530	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:59994474..59997876-chr5:60455928..60460228,5	K562	blood:
2	chr5:59995106..59997535-chr5:60240120..60242292,3	K562	blood:
3	chr5:59995886..59998322-chr5:60239584..60242446,2	MCF-7	breast:
4	chr5:59996423..59998684-chr5:60001090..60003995,3	MCF-7	breast:

Variant related genes	Relation type
DEPDC1B	TF binding region
ENSG00000049167	Chromatin interaction
ENSG00000188725	Chromatin interaction
ENSG00000164182	Chromatin interaction
ENSG00000251279	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv1816307	chr5:59992305-60012235	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv1794154	chr5:59995393-60012235	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv1821070	chr5:59995393-60012235	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv1801919	chr5:59995393-60013913	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59994200-59996800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:59994400-59996800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:59994400-59996800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:59994400-59997000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr5:59994600-59996800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:59994600-59996800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr5:59994600-59996800	Active TSS	NHLF	lung
8	chr5:59994800-59996800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:59994800-59996800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:59994800-59996800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:59994800-59996800	Active TSS	HSMM	muscle
12	chr5:59994800-59996800	Active TSS	HSMMtube	muscle
13	chr5:59994800-59996800	Active TSS	NHDF-Ad	bronchial
14	chr5:59994800-59997000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr5:59994800-59997000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:59994800-59997000	Active TSS	Fetal Brain Female	brain
17	chr5:59994800-59997000	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr5:59995000-59996800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:59995000-59996800	Active TSS	Colonic Mucosa	Colon
20	chr5:59995000-59996800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr5:59995000-59996800	Active TSS	Fetal Muscle Trunk	muscle
22	chr5:59995000-59996800	Active TSS	Fetal Stomach	stomach
23	chr5:59995000-59996800	Active TSS	Rectal Smooth Muscle	rectum
24	chr5:59995200-59996800	Active TSS	Brain Hippocampus Middle	brain
25	chr5:59995200-59996800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:59995200-59996800	Active TSS	Ovary	ovary
27	chr5:59995200-59996800	Active TSS	Psoas Muscle	Psoas
28	chr5:59995200-59996800	Active TSS	A549	lung
29	chr5:59995200-59997000	Active TSS	Brain Angular Gyrus	brain
30	chr5:59995200-59997000	Active TSS	Right Ventricle	heart
31	chr5:59995400-59996800	Active TSS	Aorta	Aorta
32	chr5:59995600-59996800	Active TSS	Colon Smooth Muscle	Colon
33	chr5:59995600-59996800	Active TSS	Duodenum Mucosa	Duodenum
34	chr5:59995600-59997000	Active TSS	Brain Anterior Caudate	brain
35	chr5:59996000-59996800	Active TSS	Stomach Smooth Muscle	stomach
36	chr5:59996200-59996800	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr5:59996200-59996800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr5:59996200-59996800	Active TSS	Right Atrium	heart
39	chr5:59996200-59996800	Flanking Active TSS	Hela-S3	cervix
40	chr5:59996200-59997000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:59996200-59997000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr5:59996200-59997000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:59996200-59997000	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr5:59996200-59997000	Flanking Active TSS	Dnd41	blood
45	chr5:59996200-59997000	Flanking Active TSS	HMEC	breast
46	chr5:59996200-59997200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:59996400-59996800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr5:59996400-59996800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr5:59996400-59996800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:59996400-59996800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links