Variant report

Variant	rs11609078
Chromosome Location	chr12:45263390-45263391
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10506260	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11609889	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11612170	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11612586	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11613494	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11614127	0.82[CEU][hapmap]
rs11614600	0.82[EUR][1000 genomes]
rs11615455	0.81[EUR][1000 genomes]
rs12810186	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12811419	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12811488	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12813393	0.93[EUR][1000 genomes]
rs12816104	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12816234	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12816596	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12818196	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12822209	0.81[EUR][1000 genomes]
rs12822384	0.85[CEU][hapmap]
rs12829582	0.81[EUR][1000 genomes]
rs12830481	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs12831193	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1605295	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17095316	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17598279	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2135546	0.82[CEU][hapmap]
rs28696281	0.83[EUR][1000 genomes]
rs34073769	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34089464	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34568257	0.81[EUR][1000 genomes]
rs34608296	0.85[EUR][1000 genomes]
rs34685472	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35018588	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35256979	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35374916	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35514455	0.85[EUR][1000 genomes]
rs35555451	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35781370	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35799097	0.81[EUR][1000 genomes]
rs35939831	0.85[EUR][1000 genomes]
rs71459269	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459270	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71459276	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs71459279	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71459290	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71459292	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45257000-45266800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:45257400-45265200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:45258600-45265600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:45258600-45267800	Weak transcription	Brain Germinal Matrix	brain
5	chr12:45259600-45266000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:45260000-45268000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:45260400-45264000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:45261200-45264800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:45261200-45265400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:45262000-45267800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr12:45262600-45264000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:45262800-45263400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:45263000-45264000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:45263000-45269000	Active TSS	Fetal Brain Female	brain
15	chr12:45263200-45263600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
16	chr12:45263200-45263800	Weak transcription	Fetal Brain Male	brain
17	chr12:45263200-45264000	Enhancers	Primary T helper cells PMA-I stimulated	--

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