Variant report

Variant	rs11060065
Chromosome Location	chr12:123286491-123286492
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	chr12:123278724..123280255-chr12:123285418..123287596,2	MCF-7	breast:
2	chr12:123285953..123287953-chr12:123322856..123324793,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10773627	0.82[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs11059711	0.81[CHB][hapmap]
rs11060064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060208	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11060209	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11060762	1.00[MEX][hapmap]
rs12255	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs12297553	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12298293	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12298664	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12299742	0.84[ASN][1000 genomes]
rs12303328	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs12305822	0.81[CHB][hapmap]
rs12307038	0.81[CHB][hapmap];0.91[GIH][hapmap]
rs12310386	0.81[CHB][hapmap]
rs12312837	0.81[CHB][hapmap];0.91[GIH][hapmap]
rs12313006	0.95[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs12313538	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12313600	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12314494	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12314544	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12314976	1.00[CEU][hapmap]
rs12315520	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12318871	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12319654	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12321100	0.81[ASN][1000 genomes]
rs12321131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321556	0.81[CHB][hapmap]
rs1671685	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1696326	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1696349	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1799618	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1979236	0.86[ASN][1000 genomes]
rs1979237	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2100500	0.86[ASN][1000 genomes]
rs2135014	0.87[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs2271050	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs2271051	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap]
rs2292131	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2292134	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs2292136	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs2292139	0.86[AMR][1000 genomes]
rs2649908	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2649909	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3782289	1.00[MEX][hapmap]
rs3817095	0.81[CHB][hapmap]
rs3825143	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs3852537	0.81[CHB][hapmap]
rs4759355	0.86[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4759382	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs4759389	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs4759392	0.95[ASN][1000 genomes]
rs4759393	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs56272219	0.86[ASN][1000 genomes]
rs58182048	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59922385	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60308342	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7138398	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs7294991	0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7303024	0.86[ASN][1000 genomes]
rs7309225	0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7311386	0.81[CHB][hapmap]
rs73421642	0.86[ASN][1000 genomes]
rs735378	0.86[ASN][1000 genomes]
rs754080	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs839360	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs897386	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs897391	0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs897393	0.82[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs921808	0.82[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs937520	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9788290	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11060065	BCL7A	cis	lymphoblastoid	seeQTL
rs11060065	GPR109B	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123259400-123310600	Weak transcription	HSMMtube	muscle
2	chr12:123259800-123310600	Weak transcription	Brain Substantia Nigra	brain
3	chr12:123260000-123303600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:123264200-123290800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:123265600-123303600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:123266000-123303800	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:123274600-123288800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:123278600-123305600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:123284400-123297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:123284600-123288800	Weak transcription	Gastric	stomach
11	chr12:123284600-123291000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:123284800-123293400	Weak transcription	Primary B cells from cord blood	blood
13	chr12:123284800-123297600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:123284800-123297600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:123285800-123286600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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