Variant report

Variant	rs555346066
Chromosome Location	chr5:79949880-79949881
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	POLR2A	chr5:79949416-79951701	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:79949816-79951683	Raji	blood:	n/a	n/a
3	JUND	chr5:79949879-79950074	K562	blood:	n/a	n/a
4	POLR2A	chr5:79949826-79951549	GM19193	blood:	n/a	n/a
5	SIN3A	chr5:79949104-79951221	H1-hESC	embryonic stem cell:	n/a	chr5:79950816-79950827 chr5:79949531-79949539
6	POLR2A	chr5:79949794-79951638	MCF-7	breast:	n/a	n/a
7	POLR2A	chr5:79949851-79951173	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr5:79949856-79951727	GM19099	blood:	n/a	n/a
9	TAF1	chr5:79949869-79951146	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3AK20	chr5:79949748-79951402	MCF-7	breast:	n/a	n/a
11	POLR2A	chr5:79948603-79951714	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:79949736-79951618	GM12878	blood:	n/a	n/a
13	EBF1	chr5:79949828-79950319	GM12878	blood:	n/a	n/a
14	CCNT2	chr5:79949448-79951322	K562	blood:	n/a	chr5:79950385-79950394 chr5:79950824-79950833 chr5:79950816-79950825
15	TBP	chr5:79949866-79951226	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr5:79949798-79951220	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr5:79949810-79951741	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:79949192-79951540	K562	blood:	n/a	n/a
19	TEAD4	chr5:79949317-79949954	K562	blood:	n/a	n/a
20	POLR2A	chr5:79949770-79951251	K562	blood:	n/a	n/a
21	TAL1	chr5:79949235-79949955	K562	blood:	n/a	n/a
22	POLR2A	chr5:79949470-79951611	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr5:79949759-79951597	Hela-S3	cervix:	n/a	n/a
24	HEY1	chr5:79949698-79950412	HepG2	liver:	n/a	n/a
25	MXI1	chr5:79949415-79950055	K562	blood:	n/a	n/a
26	POLR2A	chr5:79949879-79951586	GM12878	blood:	n/a	n/a
27	YY1	chr5:79949854-79951083	HepG2	liver:	n/a	chr5:79950115-79950129 chr5:79950849-79950858 chr5:79950385-79950394 chr5:79950824-79950833 chr5:79950816-79950827 chr5:79950380-79950394 chr5:79950805-79950824
28	POLR2A	chr5:79949857-79951163	HL-60	blood:	n/a	n/a
29	MXI1	chr5:79949861-79951449	HepG2	liver:	n/a	n/a
30	GATA1	chr5:79949269-79950195	PBDE	blood:	n/a	chr5:79949511-79949532 chr5:79949518-79949525 chr5:79949517-79949527 chr5:79949515-79949525 chr5:79949518-79949527
31	POLR2A	chr5:79949737-79951753	K562	blood:	n/a	n/a
32	ZMIZ1	chr5:79949346-79949933	K562	blood:	n/a	n/a
33	MAX	chr5:79949774-79951121	K562	blood:	n/a	n/a
34	HA-E2F1	chr5:79949798-79951102	MCF-7	breast:	n/a	chr5:79950516-79950526 chr5:79950368-79950375 chr5:79950852-79950861 chr5:79950367-79950376 chr5:79950368-79950375 chr5:79950824-79950833 chr5:79950368-79950375 chr5:79950385-79950394
35	POLR2A	chr5:79949856-79951240	K562	blood:	n/a	n/a
36	HNF4A	chr5:79949779-79950164	HepG2	liver:	n/a	chr5:79949986-79950001 chr5:79949988-79950000 chr5:79949988-79950000 chr5:79949986-79950001 chr5:79949986-79950001
37	POLR2A	chr5:79949099-79952397	GM12891	blood:	n/a	n/a
38	HNF4G	chr5:79949759-79950162	HepG2	liver:	n/a	chr5:79949986-79950001 chr5:79949988-79950000 chr5:79949988-79950000 chr5:79950013-79950028 chr5:79949987-79950002 chr5:79949986-79950001
39	POLR2A	chr5:79949765-79951202	H1-hESC	embryonic stem cell:	n/a	n/a
40	TFAP2A	chr5:79949697-79950257	Hela-S3	cervix:	n/a	n/a
41	SMARCB1	chr5:79949821-79951064	Hela-S3	cervix:	n/a	n/a
42	TBP	chr5:79949385-79951317	K562	blood:	n/a	n/a
43	POLR2A	chr5:79949799-79951254	GM18526	blood:	n/a	n/a
44	POLR2A	chr5:79949879-79950231	GM12878	blood:	n/a	n/a
45	ELF1	chr5:79949864-79951108	GM12878	blood:	n/a	chr5:79950849-79950858
46	POLR2A	chr5:79949873-79951522	NB4	blood:	n/a	n/a
47	MAX	chr5:79949873-79950901	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr5:79949356-79951526	Hela-S3	cervix:	n/a	n/a
49	HNF4A	chr5:79949803-79950085	HepG2	liver:	n/a	chr5:79949986-79950001 chr5:79949988-79950000 chr5:79949988-79950000 chr5:79949986-79950001 chr5:79949986-79950001
50	TFAP2C	chr5:79949770-79951054	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:79781713..79786255-chr5:79948613..79954295,12	MCF-7	breast:
2	chr5:79782822..79786705-chr5:79948261..79952248,11	MCF-7	breast:
3	chr5:79918045..79920951-chr5:79949482..79951097,2	MCF-7	breast:
4	chr5:79702114..79706204-chr5:79947823..79953616,8	MCF-7	breast:

Variant related genes	Relation type
DHFR	TF binding region
MSH3	TF binding region
MTRNR2L2	TF binding region
ENSG00000249042	Chromatin interaction
ENSG00000039319	Chromatin interaction
ENSG00000152380	Chromatin interaction
ENSG00000251221	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3406922	chr5:79949421-79951969	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79937000-79950000	Weak transcription	Ovary	ovary
2	chr5:79948600-79950200	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr5:79948600-79951200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr5:79948600-79952000	Active TSS	GM12878-XiMat	blood
5	chr5:79948800-79951400	Active TSS	Fetal Intestine Large	intestine
6	chr5:79949000-79950000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:79949000-79950000	Enhancers	Spleen	Spleen
8	chr5:79949000-79950200	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr5:79949000-79950200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:79949000-79950200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:79949000-79950200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:79949000-79950200	Flanking Active TSS	Liver	Liver
13	chr5:79949000-79950200	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr5:79949000-79950200	Flanking Active TSS	HUVEC	blood vessel
15	chr5:79949000-79951200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:79949000-79951200	Active TSS	Stomach Mucosa	stomach
17	chr5:79949000-79951400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr5:79949000-79951400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr5:79949000-79951400	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr5:79949000-79951400	Active TSS	Fetal Intestine Small	intestine
21	chr5:79949000-79951600	Active TSS	A549	lung
22	chr5:79949200-79950000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:79949200-79950000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr5:79949200-79950000	Flanking Active TSS	Fetal Heart	heart
25	chr5:79949200-79950000	Flanking Active TSS	Thymus	Thymus
26	chr5:79949200-79950000	Flanking Active TSS	NH-A	brain
27	chr5:79949200-79950200	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr5:79949200-79950200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr5:79949200-79950200	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr5:79949200-79950200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr5:79949200-79950200	Flanking Active TSS	Fetal Brain Female	brain
32	chr5:79949200-79950200	Flanking Active TSS	Fetal Stomach	stomach
33	chr5:79949200-79950200	Flanking Active TSS	Fetal Thymus	thymus
34	chr5:79949200-79950200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr5:79949200-79951200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:79949200-79951200	Active TSS	Brain Cingulate Gyrus	brain
37	chr5:79949200-79951400	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr5:79949200-79951400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:79949200-79951400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:79949200-79951600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr5:79949200-79951600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:79949200-79951600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr5:79949200-79951600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:79949200-79952000	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr5:79949400-79950000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:79949400-79950000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr5:79949400-79950000	Flanking Active TSS	Fetal Lung	lung
48	chr5:79949400-79950000	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr5:79949400-79950000	Active TSS	Right Atrium	heart
50	chr5:79949400-79950000	Flanking Active TSS	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links