Variant report

Variant	rs888823
Chromosome Location	chr5:80253054-80253055
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	GATA3	chr5:80252722-80253558	MCF-7	breast:	n/a	n/a
2	MAZ	chr5:80252936-80253179	HepG2	liver:	n/a	n/a
3	EP300	chr5:80252810-80253209	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOXA1	chr5:80252810-80253173	HepG2	liver:	n/a	n/a
5	MAX	chr5:80252967-80253114	HepG2	liver:	n/a	n/a
6	FOXA2	chr5:80252609-80253213	HepG2	liver:	n/a	n/a
7	NFIC	chr5:80252779-80253180	HepG2	liver:	n/a	n/a
8	TEAD4	chr5:80252781-80253274	H1-hESC	embryonic stem cell:	n/a	n/a
9	EP300	chr5:80252930-80253209	HepG2	liver:	n/a	n/a
10	CHD2	chr5:80252913-80253132	H1-hESC	embryonic stem cell:	n/a	n/a
11	RCOR1	chr5:80252944-80253108	HepG2	liver:	n/a	n/a
12	EP300	chr5:80252872-80253189	H1-hESC	embryonic stem cell:	n/a	n/a
13	FOXA1	chr5:80252666-80253189	HepG2	liver:	n/a	n/a
14	NANOG	chr5:80252940-80253194	H1-hESC	embryonic stem cell:	n/a	chr5:80253018-80253032
15	JUND	chr5:80252638-80253346	H1-hESC	embryonic stem cell:	n/a	chr5:80253057-80253069 chr5:80253232-80253244
16	ARID3A	chr5:80252820-80253186	HepG2	liver:	n/a	n/a
17	BCL11A	chr5:80252895-80253149	H1-hESC	embryonic stem cell:	n/a	n/a
18	FOXA2	chr5:80252849-80253128	A549	lung:	n/a	n/a
19	SIN3A	chr5:80252765-80253126	H1-hESC	embryonic stem cell:	n/a	n/a
20	FOXA1	chr5:80252704-80253295	HepG2	liver:	n/a	n/a
21	ZNF143	chr5:80253039-80253396	H1-hESC	embryonic stem cell:	n/a	n/a
22	TEAD4	chr5:80252831-80253212	H1-hESC	embryonic stem cell:	n/a	n/a
23	USF1	chr5:80252866-80253168	H1-hESC	embryonic stem cell:	n/a	n/a
24	FOXA2	chr5:80252816-80253124	HepG2	liver:	n/a	n/a
25	POU5F1	chr5:80252793-80253192	H1-hESC	embryonic stem cell:	n/a	chr5:80253056-80253070 chr5:80253056-80253070 chr5:80252993-80253007 chr5:80253000-80253008 chr5:80253056-80253070
26	GATA3	chr5:80252709-80253424	MCF-7	breast:	n/a	n/a
27	HDAC2	chr5:80252710-80253144	H1-hESC	embryonic stem cell:	n/a	chr5:80252899-80252913 chr5:80252904-80252918
28	CEBPB	chr5:80252917-80253299	H1-hESC	embryonic stem cell:	n/a	n/a
29	SP1	chr5:80252759-80253270	H1-hESC	embryonic stem cell:	n/a	n/a
30	CEBPB	chr5:80252810-80253125	HepG2	liver:	n/a	n/a
31	FOXA1	chr5:80252798-80253144	HepG2	liver:	n/a	n/a
32	FOXA1	chr5:80252883-80253078	T-47D	breast:	n/a	n/a
33	EP300	chr5:80252812-80253181	HepG2	liver:	n/a	n/a
34	HDAC2	chr5:80252831-80253172	HepG2	liver:	n/a	chr5:80252899-80252913 chr5:80252904-80252918
35	NANOG	chr5:80252862-80253136	H1-hESC	embryonic stem cell:	n/a	chr5:80252904-80252918 chr5:80253018-80253032
36	TEAD4	chr5:80252702-80253255	HepG2	liver:	n/a	n/a
37	CTCF	chr5:80253020-80253170	HEK293	kidney:	n/a	n/a
38	TCF12	chr5:80252715-80253211	H1-hESC	embryonic stem cell:	n/a	chr5:80253042-80253050
39	POU5F1	chr5:80252860-80253164	H1-hESC	embryonic stem cell:	n/a	chr5:80253056-80253070 chr5:80253056-80253070 chr5:80252993-80253007 chr5:80253000-80253008 chr5:80253056-80253070
40	TCF12	chr5:80252826-80253146	H1-hESC	embryonic stem cell:	n/a	chr5:80253042-80253050
41	BACH1	chr5:80252785-80253258	H1-hESC	embryonic stem cell:	n/a	n/a
42	HDAC2	chr5:80252911-80253186	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RASGRF2	TF binding region
ENSG00000251450	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10491488	0.99[ASN][1000 genomes]
rs10491490	0.99[ASN][1000 genomes]
rs12522495	0.99[ASN][1000 genomes]
rs12653956	0.83[ASN][1000 genomes]
rs59989282	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66484258	0.97[ASN][1000 genomes]
rs6893705	0.82[ASN][1000 genomes]
rs888822	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80249000-80255000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:80251000-80253800	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr5:80251600-80255800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:80251800-80253400	Bivalent Enhancer	Brain Germinal Matrix	brain
5	chr5:80252000-80254000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:80252200-80253400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:80252200-80254000	Enhancers	Primary T cells from cord blood	blood
8	chr5:80252400-80253400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:80252400-80253600	Enhancers	HepG2	liver
10	chr5:80252400-80254000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:80252400-80254000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:80252400-80255600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:80252400-80255600	Weak transcription	Ovary	ovary
14	chr5:80252600-80254000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:80252600-80255400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr5:80252800-80253200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:80252800-80255600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr5:80253000-80253200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:80253000-80253200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr5:80253000-80253200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr5:80253000-80253200	Enhancers	Brain Hippocampus Middle	brain
22	chr5:80253000-80253400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr5:80253000-80255000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr5:80253000-80255200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:80253000-80255200	Weak transcription	Brain Substantia Nigra	brain
26	chr5:80253000-80255200	Enhancers	Thymus	Thymus
27	chr5:80253000-80255400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links