Variant report

Variant	rs1458165
Chromosome Location	chr12:41822199-41822200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1026462	0.96[CEU][hapmap]
rs1026464	0.81[CEU][hapmap]
rs10785264	0.80[JPT][hapmap]
rs10785265	0.96[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs10785266	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs10880071	0.88[CHD][hapmap]
rs10880073	0.80[JPT][hapmap];0.86[AFR][1000 genomes]
rs10880075	0.81[AMR][1000 genomes]
rs10880076	0.95[CEU][hapmap]
rs11180934	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs1155220	0.81[AMR][1000 genomes]
rs1160183	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs1160184	0.95[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs1160748	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs1160749	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs12314238	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1350429	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1350430	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1379763	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1379768	0.96[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs1379769	0.88[CEU][hapmap]
rs1379774	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1379775	0.80[JPT][hapmap]
rs1379776	0.81[AMR][1000 genomes]
rs1458156	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs1458157	0.81[CEU][hapmap]
rs1458158	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs1458159	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1458166	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1458167	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs1458168	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs1471161	0.87[ASW][hapmap];0.96[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs1471162	0.81[AMR][1000 genomes]
rs1471163	0.81[AMR][1000 genomes]
rs1551593	0.96[CEU][hapmap];0.84[CHB][hapmap]
rs1551595	0.81[AMR][1000 genomes]
rs1551596	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs1598894	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs1841025	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs1870285	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1870286	0.87[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs2125287	0.91[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap]
rs2250009	0.85[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs2250908	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2251259	0.81[AMR][1000 genomes]
rs2251349	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs2251683	0.81[AMR][1000 genomes]
rs2251684	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs2255035	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs2255145	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs2264905	0.81[AMR][1000 genomes]
rs2405919	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs2446143	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs2446144	0.85[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs2468314	0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2468315	0.88[CEU][hapmap]
rs2468317	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs2608692	0.87[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs2608696	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2608697	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2608701	0.81[AMR][1000 genomes]
rs2608702	0.91[CEU][hapmap]
rs2608703	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2608704	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2608706	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2608707	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2608708	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2608710	0.81[AMR][1000 genomes]
rs2608711	0.84[CEU][hapmap]
rs2608715	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2608718	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2730803	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs2730805	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2730807	0.83[CHB][hapmap]
rs2730809	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs2730811	0.80[AMR][1000 genomes]
rs2730814	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs2730817	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs2730819	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs2730820	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs2730821	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs2730822	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs2730828	0.87[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs2730829	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs2730830	0.96[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs2733269	0.87[MEX][hapmap]
rs2733274	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.90[LWK][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs2733275	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2733278	0.85[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2733282	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs2733287	0.81[CEU][hapmap]
rs2733289	0.96[CEU][hapmap];0.80[AMR][1000 genomes]
rs2733291	0.81[AMR][1000 genomes]
rs2733292	0.80[AMR][1000 genomes]
rs2733293	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs2733297	0.81[AMR][1000 genomes]
rs2733298	0.87[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs2733299	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs285556	0.82[MEX][hapmap]
rs285575	0.81[MEX][hapmap]
rs2957590	0.81[AMR][1000 genomes]
rs35766123	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4584644	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs4768353	0.81[AMR][1000 genomes]
rs7298808	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs7977318	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs897973	0.87[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs971998	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs981012	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs981014	0.96[CEU][hapmap]
rs989904	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs996356	0.87[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][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	nsv832383	chr12:41693298-41846934	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
2	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
3	nsv1037987	chr12:41815867-41840251	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1458165	PDZRN4	cis	occipital cortex	BrainEAC
rs1458165	PDZRN4	cis	temporal cortex	BrainEAC

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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