Variant report

Variant	rs10880085
Chromosome Location	chr12:41903420-41903421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10219633	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10506194	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10506196	0.89[CHB][hapmap]
rs10785234	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10880037	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10880068	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10880069	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10880070	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10880080	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10880083	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10880084	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10880090	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180782	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11180829	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180830	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180833	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180840	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180841	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180844	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180845	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180849	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180852	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180855	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180868	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180873	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180874	1.00[CHB][hapmap]
rs11180875	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180879	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180883	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180894	0.81[ASN][1000 genomes]
rs11180902	0.83[ASN][1000 genomes]
rs11180903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11180904	0.83[ASN][1000 genomes]
rs11180910	0.86[ASN][1000 genomes]
rs11180913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11180915	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11180921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11180922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11180928	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11180944	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180945	0.96[ASN][1000 genomes]
rs11180947	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180949	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180950	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180952	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180954	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11180955	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11180959	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180962	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180963	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180964	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11180965	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180966	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180967	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180968	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180969	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180970	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180972	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180973	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180974	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180975	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180976	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180978	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs11180983	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11180989	0.81[JPT][hapmap]
rs11180995	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180997	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11181000	0.89[CHB][hapmap]
rs11181010	0.82[JPT][hapmap]
rs12227540	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12228172	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12230294	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12231433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12231803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12232019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12582204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12582987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1379766	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1458153	0.81[JPT][hapmap]
rs1458172	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs1458173	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs17129417	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17129436	0.88[CHB][hapmap]
rs17835484	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs1918230	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2125289	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs3214027	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs725527	0.81[JPT][hapmap]
rs7299395	0.82[JPT][hapmap]
rs7968280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7969769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7979435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9652045	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv826349	chr12:41878846-41911495	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 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	chr12:41869600-41905200	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:41877400-41903600	Weak transcription	Ovary	ovary
3	chr12:41898600-41915400	Weak transcription	Aorta	Aorta
4	chr12:41899000-41906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:41900600-41903800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:41900600-41904000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr12:41902000-41903600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:41902000-41909400	Enhancers	Brain Germinal Matrix	brain
9	chr12:41902200-41908000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:41902400-41907400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:41902400-41907800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:41902400-41915000	Weak transcription	Brain Anterior Caudate	brain
13	chr12:41902600-41907600	Weak transcription	Brain Substantia Nigra	brain
14	chr12:41902600-41907800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:41902600-41907800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:41903200-41903800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:41903400-41904600	Weak transcription	Brain Hippocampus Middle	brain

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