Variant report

Variant	rs12339490
Chromosome Location	chr9:93298950-93298951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93298847..93301610-chr9:93304161..93305882,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10121938	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512200	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993558	0.88[EUR][1000 genomes]
rs10993559	0.88[EUR][1000 genomes]
rs10993560	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10993561	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10993562	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10993571	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12338796	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12339278	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12339449	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12340368	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12343716	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349410	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351665	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13440327	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17451922	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021025	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7025381	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7036767	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042807	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs919105	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs970686	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv893565	chr9:93130796-93392332	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv893566	chr9:93209923-93439259	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93296800-93299800	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr9:93297000-93299400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:93297000-93300000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr9:93297400-93299200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:93297600-93300000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr9:93297800-93300000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr9:93298000-93299800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr9:93298000-93300000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr9:93298600-93299200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:93298600-93299800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr9:93298800-93299200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:93298800-93299800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links