Variant report

Variant	rs12409592
Chromosome Location	chr1:76317549-76317550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 157 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs1021462	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10732724	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs10782556	0.99[ASN][1000 genomes]
rs10873724	0.80[ASN][1000 genomes]
rs10873727	0.81[ASN][1000 genomes]
rs10873728	0.81[ASN][1000 genomes]
rs10873738	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10873739	0.81[ASN][1000 genomes]
rs10873804	0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs11161439	0.84[ASN][1000 genomes]
rs11161447	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11161465	0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11161600	0.92[ASN][1000 genomes]
rs11161602	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.96[ASN][1000 genomes]
rs11161605	0.91[ASN][1000 genomes]
rs11161700	0.81[ASN][1000 genomes]
rs11161731	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11161790	0.86[ASN][1000 genomes]
rs11161795	0.86[ASN][1000 genomes]
rs11161852	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11161887	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs11164035	0.84[ASN][1000 genomes]
rs11164037	0.84[ASN][1000 genomes]
rs1144328	0.81[JPT][hapmap]
rs1144331	0.81[JPT][hapmap]
rs1144333	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1144337	0.81[JPT][hapmap]
rs1144338	0.81[ASN][1000 genomes]
rs1144342	0.81[JPT][hapmap]
rs1146635	0.84[MKK][hapmap]
rs1146647	0.81[JPT][hapmap]
rs1146648	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1146649	0.81[JPT][hapmap]
rs1146651	0.85[JPT][hapmap]
rs1146652	0.81[JPT][hapmap]
rs1146656	0.81[ASN][1000 genomes]
rs11579355	0.81[ASN][1000 genomes]
rs12021750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12022011	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12024086	0.86[ASN][1000 genomes]
rs12024645	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.99[ASN][1000 genomes]
rs12024786	0.86[ASN][1000 genomes]
rs12027620	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12031600	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12032051	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12033058	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12033059	0.99[ASN][1000 genomes]
rs12044025	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12044211	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12045299	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12045363	0.99[ASN][1000 genomes]
rs12049212	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12076093	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12078151	0.81[ASN][1000 genomes]
rs12081710	0.81[ASN][1000 genomes]
rs12090712	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12385715	0.81[ASN][1000 genomes]
rs12401729	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12405178	0.81[ASN][1000 genomes]
rs12407107	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs12410373	0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs1250876	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1250880	0.82[CHB][hapmap]
rs1251078	0.82[CHB][hapmap]
rs1251079	0.82[CHB][hapmap]
rs1251272	0.82[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1251274	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1251275	0.81[ASN][1000 genomes]
rs12563737	0.81[ASN][1000 genomes]
rs12564772	0.99[ASN][1000 genomes]
rs12567390	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs12703	0.81[JPT][hapmap]
rs12724860	0.94[ASN][1000 genomes]
rs12727156	0.91[ASN][1000 genomes]
rs12728962	0.92[ASN][1000 genomes]
rs12732495	0.86[JPT][hapmap]
rs12744608	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs12745456	0.81[ASN][1000 genomes]
rs12747967	0.84[ASN][1000 genomes]
rs12755811	0.80[ASN][1000 genomes]
rs12756349	0.92[ASN][1000 genomes]
rs12757213	0.91[ASN][1000 genomes]
rs12757866	0.87[ASN][1000 genomes]
rs1303870	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1391518	0.84[ASN][1000 genomes]
rs1391520	0.84[ASN][1000 genomes]
rs1498313	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs1603734	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1689271	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs17097634	0.99[ASN][1000 genomes]
rs17097681	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs17097695	0.82[JPT][hapmap]
rs17649675	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1796812	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs1826978	0.87[ASN][1000 genomes]
rs1908089	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2047435	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2131558	0.99[ASN][1000 genomes]
rs2307077	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs34045364	0.81[ASN][1000 genomes]
rs34177389	0.81[ASN][1000 genomes]
rs34486572	0.99[ASN][1000 genomes]
rs34984955	0.86[ASN][1000 genomes]
rs35290302	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35591768	0.81[ASN][1000 genomes]
rs35837767	0.84[ASN][1000 genomes]
rs36054685	0.82[ASN][1000 genomes]
rs3737574	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.98[ASN][1000 genomes]
rs3765682	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3795251	0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs3819949	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs4949884	0.81[ASN][1000 genomes]
rs5019550	0.81[ASN][1000 genomes]
rs56350137	0.81[ASN][1000 genomes]
rs5745314	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs5745327	0.81[JPT][hapmap]
rs5745334	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs5745343	0.81[JPT][hapmap]
rs5745353	0.94[ASN][1000 genomes]
rs5745392	0.81[JPT][hapmap]
rs5745426	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5745429	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5745448	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap]
rs5745451	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs5745464	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs5745465	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs5745523	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs5745532	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs5745542	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs5745546	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs58552356	0.97[ASN][1000 genomes]
rs6668963	0.84[ASN][1000 genomes]
rs6676182	0.81[ASN][1000 genomes]
rs6680389	0.86[ASN][1000 genomes]
rs6687882	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs6695055	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs67108483	0.84[ASN][1000 genomes]
rs71656856	0.91[ASN][1000 genomes]
rs7514912	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7516477	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7525919	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7545057	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7548391	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7548695	0.80[ASN][1000 genomes]
rs7548991	0.95[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs815301	0.82[ASN][1000 genomes]
rs815305	0.82[ASN][1000 genomes]
rs9660848	0.95[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1795237	chr1:76268573-76383565	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1800125	chr1:76269439-76379497	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1799260	chr1:76269439-76383297	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1847721	chr1:76269439-76383565	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1004669	chr1:76301198-76409451	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv871671	chr1:76304215-76391646	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12409592	MSH4	cis	cerebellum	SCAN
rs12409592	MSH4	cis	parietal	SCAN
rs12409592	ACADM	cis	parietal	SCAN

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

No data

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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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