Variant report

Variant	rs12340242
Chromosome Location	chr9:108183748-108183749
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108183002..108185027-chr9:108190016..108191824,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10115811	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10115838	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10119410	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10119483	1.00[ASW][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10121304	0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10123783	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10125150	0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10125368	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441742	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441743	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441771	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441772	0.89[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441773	0.81[ASW][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10441774	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12004028	0.83[AMR][1000 genomes]
rs12115219	0.90[MKK][hapmap]
rs12336341	0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12337845	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12338480	0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12338896	0.95[MKK][hapmap]
rs12345255	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12346497	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12348331	1.00[MEX][hapmap]
rs12348967	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12349041	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12349068	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12353548	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16924542	1.00[MEX][hapmap]
rs28456113	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28461171	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28541347	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28613030	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56965223	0.83[AMR][1000 genomes]
rs57430142	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57497195	0.83[AMR][1000 genomes]
rs7025836	1.00[MEX][hapmap]
rs7028140	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7028216	0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[AMR][1000 genomes]
rs7867378	1.00[MEX][hapmap]
rs7868841	1.00[MEX][hapmap]
rs9299388	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108176200-108188200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:108177600-108186400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:108177800-108194200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:108177800-108194200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:108179600-108184200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:108180600-108184400	Enhancers	Brain Hippocampus Middle	brain
7	chr9:108181800-108184800	Enhancers	HepG2	liver
8	chr9:108182200-108184000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:108182600-108193800	Weak transcription	Brain Angular Gyrus	brain
10	chr9:108182600-108193800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:108182800-108184000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr9:108182800-108193600	Weak transcription	Brain Substantia Nigra	brain
13	chr9:108182800-108193800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:108183000-108194000	Weak transcription	Brain Anterior Caudate	brain
15	chr9:108183600-108188000	Weak transcription	Liver	Liver

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