Variant report

Variant	rs10476889
Chromosome Location	chr5:147254646-147254647
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU5F1	chr5:147254204-147255050	H1-hESC	embryonic stem cell:	n/a	chr5:147254383-147254397 chr5:147254383-147254397
2	TBP	chr5:147253652-147254971	H1-hESC	embryonic stem cell:	n/a	n/a
3	TCF12	chr5:147254594-147254859	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr5:147253925-147255134	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP1	chr5:147253793-147255091	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr5:147246099-147256428	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:147250333-147255187	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr5:147253703-147255115	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD2	chr5:147254052-147254954	H1-hESC	embryonic stem cell:	n/a	n/a
10	JUND	chr5:147253837-147255142	H1-hESC	embryonic stem cell:	n/a	n/a
11	YY1	chr5:147254068-147255006	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr5:147254630-147254928	H1-hESC	embryonic stem cell:	n/a	n/a
13	TAF7	chr5:147253714-147254882	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF1	chr5:147254555-147254891	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr5:147254399-147254894	H1-hESC	embryonic stem cell:	n/a	n/a
16	ATF2	chr5:147253743-147255142	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr5:147254446-147255186	H1-hESC	embryonic stem cell:	n/a	n/a
18	ATF2	chr5:147253932-147255056	H1-hESC	embryonic stem cell:	n/a	n/a
19	SP4	chr5:147254047-147254939	H1-hESC	embryonic stem cell:	n/a	n/a
20	SIN3A	chr5:147253854-147254963	H1-hESC	embryonic stem cell:	n/a	n/a
21	HDAC2	chr5:147254630-147254925	H1-hESC	embryonic stem cell:	n/a	n/a
22	CHD1	chr5:147254091-147255250	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr5:147254308-147254964	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTBP2	chr5:147253930-147254702	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr5:147253715-147254949	H1-hESC	embryonic stem cell:	n/a	n/a
26	GTF2F1	chr5:147253919-147254975	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
SCGB3A2	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10071367	0.83[AFR][1000 genomes]
rs10075900	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10477353	0.94[AFR][1000 genomes]
rs10477354	0.88[AFR][1000 genomes]
rs11505126	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12171507	0.91[AFR][1000 genomes]
rs13355947	0.91[AFR][1000 genomes]
rs13356314	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13360221	0.97[AFR][1000 genomes]
rs13435996	0.94[AFR][1000 genomes]
rs13436526	0.94[AFR][1000 genomes]
rs6881482	0.86[AFR][1000 genomes]
rs73261368	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73261392	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73263243	0.86[AFR][1000 genomes]
rs73263257	0.85[AFR][1000 genomes]
rs73263261	0.84[AFR][1000 genomes]

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	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv933308	chr5:147173804-147269006	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147234200-147262400	Weak transcription	Right Atrium	heart
2	chr5:147247600-147260200	Weak transcription	Aorta	Aorta
3	chr5:147249200-147255800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:147252000-147255000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr5:147254000-147255200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:147254000-147255200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr5:147254000-147255400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr5:147254000-147256200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:147254200-147254800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:147254200-147255200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:147254200-147255200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:147254200-147255400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
13	chr5:147254200-147255400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr5:147254200-147255400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr5:147254200-147255400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr5:147254200-147255400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr5:147254400-147254800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:147254400-147254800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:147254400-147255200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:147254600-147254800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr5:147254600-147255200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:147254600-147257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links