Variant report

Variant	rs1458173
Chromosome Location	chr12:41902513-41902514
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10219633	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs10506194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10506196	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs10785234	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10880037	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs10880068	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10880069	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs10880070	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10880080	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs10880083	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10880084	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880085	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs10880090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880097	0.91[JPT][hapmap]
rs10880101	0.91[JPT][hapmap]
rs10880102	0.91[JPT][hapmap]
rs11180782	0.89[CHB][hapmap]
rs11180829	0.81[JPT][hapmap]
rs11180830	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180833	0.88[CHB][hapmap]
rs11180840	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180841	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180844	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180845	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180849	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11180852	0.86[CHB][hapmap]
rs11180860	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs11180868	0.88[CHB][hapmap]
rs11180873	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs11180874	0.88[CHB][hapmap]
rs11180875	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180879	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180883	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180886	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180903	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180913	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180915	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11180917	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180921	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs11180922	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs11180928	0.89[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11180932	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11180935	0.89[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11180938	0.86[ASN][1000 genomes]
rs11180941	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11180944	0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs11180946	0.86[ASN][1000 genomes]
rs11180947	0.89[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11180948	0.89[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11180949	0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs11180950	0.82[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11180952	0.89[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11180953	0.89[ASN][1000 genomes]
rs11180954	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs11180955	0.81[JPT][hapmap]
rs11180957	0.89[ASN][1000 genomes]
rs11180959	0.89[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs11180962	0.88[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs11180963	0.88[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs11180964	0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs11180965	0.89[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs11180966	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs11180967	0.89[CHB][hapmap];1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11180968	0.89[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs11180969	0.89[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11180970	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180971	1.00[EUR][1000 genomes]
rs11180972	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180973	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180974	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180975	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180976	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180978	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180982	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11180983	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11180989	1.00[JPT][hapmap]
rs11180995	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11180997	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11181000	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11181005	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11181010	0.91[JPT][hapmap]
rs12227303	0.92[JPT][hapmap]
rs12227540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12228172	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12230294	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12231433	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12231803	0.89[CHB][hapmap]
rs12232019	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12581707	0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582035	0.89[ASN][1000 genomes]
rs12582204	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12582909	0.92[JPT][hapmap]
rs12582987	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs1379766	0.89[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs1458153	1.00[JPT][hapmap]
rs1458172	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17129417	0.89[CHB][hapmap];0.89[ASN][1000 genomes]
rs17129436	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17129470	0.91[JPT][hapmap]
rs17835484	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1918230	0.89[CHB][hapmap]
rs2125289	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252312	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285578	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs3214027	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs4635145	1.00[EUR][1000 genomes]
rs59955144	1.00[EUR][1000 genomes]
rs6582337	1.00[EUR][1000 genomes]
rs713288	1.00[EUR][1000 genomes]
rs725527	1.00[JPT][hapmap]
rs7968280	0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7969769	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs7979435	0.89[CHB][hapmap]
rs9652045	0.88[CHB][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:20 , 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	chr12:41901400-41902600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:41901400-41902600	Enhancers	Brain Substantia Nigra	brain
9	chr12:41902000-41902600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr12:41902000-41902600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr12:41902000-41902600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:41902000-41902600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr12:41902000-41903600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:41902000-41909400	Enhancers	Brain Germinal Matrix	brain
15	chr12:41902200-41902600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr12:41902200-41903400	Enhancers	Brain Hippocampus Middle	brain
17	chr12:41902200-41908000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:41902400-41907400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:41902400-41907800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:41902400-41915000	Weak transcription	Brain Anterior Caudate	brain

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