Variant report

Variant	rs66683260
Chromosome Location	chr5:89923923-89923924
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	FOS	chr5:89923883-89923984	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr5:89923811-89924058	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr5:89923917-89923987	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr5:89923889-89924044	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
GPR98	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10056775	0.89[EUR][1000 genomes]
rs10514330	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11738461	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11738532	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11739825	0.80[EUR][1000 genomes]
rs11739958	0.85[EUR][1000 genomes]
rs11742844	0.80[EUR][1000 genomes]
rs11745908	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11748911	0.96[EUR][1000 genomes]
rs11749693	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13157270	0.85[EUR][1000 genomes]
rs13159048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13164404	0.96[EUR][1000 genomes]
rs13167847	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13171056	0.85[EUR][1000 genomes]
rs13171303	0.82[EUR][1000 genomes]
rs13174505	0.83[EUR][1000 genomes]
rs13182944	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13183331	0.85[EUR][1000 genomes]
rs13186124	0.96[EUR][1000 genomes]
rs13190272	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16868809	0.86[AFR][1000 genomes]
rs17541517	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17541704	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17541912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17542086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17542921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17543150	0.96[EUR][1000 genomes]
rs17552645	0.82[EUR][1000 genomes]
rs17614588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17621038	0.96[EUR][1000 genomes]
rs17621160	0.96[EUR][1000 genomes]
rs17621985	0.85[EUR][1000 genomes]
rs17622555	0.85[EUR][1000 genomes]
rs28399862	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28429067	0.86[AFR][1000 genomes]
rs34301936	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34490215	0.89[EUR][1000 genomes]
rs34719862	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34774423	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35312877	0.85[EUR][1000 genomes]
rs35667071	0.96[EUR][1000 genomes]
rs35680172	0.85[EUR][1000 genomes]
rs35980777	0.84[EUR][1000 genomes]
rs36045161	0.85[EUR][1000 genomes]
rs67956713	0.83[EUR][1000 genomes]
rs6866075	0.80[EUR][1000 genomes]
rs71637308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][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	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS 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	58 gene(s)	inside rSNPs	diseases
4	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS 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

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89909800-89926400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:89909800-89928800	Weak transcription	Fetal Brain Female	brain
3	chr5:89910000-89927000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:89910000-89928600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:89914200-89927000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:89914200-89928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:89916800-89925600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:89917000-89927000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:89917400-89926200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:89918000-89950600	Weak transcription	Pancreas	Pancrea
11	chr5:89918200-89924400	Weak transcription	K562	blood
12	chr5:89918200-89925800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:89919000-89925600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:89919400-89925800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:89919600-89936400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:89920800-89925400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:89920800-89928800	Weak transcription	Brain Anterior Caudate	brain
18	chr5:89922400-89925400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr5:89922800-89928600	Weak transcription	Brain Germinal Matrix	brain
20	chr5:89923200-89924400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:89923200-89925200	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr5:89923600-89924400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:89923600-89927000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links