Variant report

Variant	rs5745448
Chromosome Location	chr1:76344705-76344706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 155 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1021462	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10732724	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10782556	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10873724	0.81[ASN][1000 genomes]
rs10873727	0.82[ASN][1000 genomes]
rs10873728	0.82[ASN][1000 genomes]
rs10873738	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10873739	0.82[ASN][1000 genomes]
rs10873804	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11161439	0.81[ASN][1000 genomes]
rs11161447	0.95[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs11161465	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs11161600	0.86[ASN][1000 genomes]
rs11161602	0.95[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11161605	0.85[ASN][1000 genomes]
rs11161700	0.82[ASN][1000 genomes]
rs11161731	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11161790	0.87[ASN][1000 genomes]
rs11161795	0.87[ASN][1000 genomes]
rs11161852	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11161887	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs11164035	0.81[ASN][1000 genomes]
rs11164037	0.81[ASN][1000 genomes]
rs1144328	0.81[JPT][hapmap]
rs1144331	0.81[JPT][hapmap]
rs1144333	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1144337	0.81[JPT][hapmap]
rs1144338	0.82[ASN][1000 genomes]
rs1144342	0.81[JPT][hapmap]
rs1146635	0.85[GIH][hapmap];0.93[MKK][hapmap]
rs1146647	0.80[JPT][hapmap]
rs1146648	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1146649	0.81[JPT][hapmap]
rs1146651	0.85[JPT][hapmap]
rs1146652	0.81[JPT][hapmap]
rs1146656	0.82[ASN][1000 genomes]
rs11579355	0.82[ASN][1000 genomes]
rs12021750	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022011	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs12024086	0.87[ASN][1000 genomes]
rs12024645	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12024786	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12027620	0.95[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs12031600	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12032051	0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12033058	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12033059	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12044025	0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12044211	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12045299	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs12045363	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12049212	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12076093	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12078151	0.82[ASN][1000 genomes]
rs12081710	0.82[ASN][1000 genomes]
rs12090712	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12164500	0.82[CEU][hapmap]
rs12385715	0.82[ASN][1000 genomes]
rs12401729	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12403889	0.82[ASN][1000 genomes]
rs12405178	0.82[ASN][1000 genomes]
rs12407107	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12409592	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap]
rs12410373	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1250876	0.80[JPT][hapmap]
rs1250880	0.80[JPT][hapmap]
rs1251272	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs1251274	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1251275	0.82[ASN][1000 genomes]
rs12564772	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12567390	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs12703	0.81[JPT][hapmap]
rs12724860	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12727156	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12728962	0.86[ASN][1000 genomes]
rs12732495	0.86[JPT][hapmap]
rs12744608	0.85[CHB][hapmap]
rs12747967	0.81[ASN][1000 genomes]
rs12756349	0.86[ASN][1000 genomes]
rs12757213	0.86[ASN][1000 genomes]
rs12757866	0.82[ASN][1000 genomes]
rs1303870	0.86[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]
rs1391518	0.81[ASN][1000 genomes]
rs1391520	0.81[ASN][1000 genomes]
rs1498313	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs1603734	0.85[JPT][hapmap]
rs1689271	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs17097634	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17097681	0.81[JPT][hapmap]
rs17097695	0.81[JPT][hapmap]
rs17649675	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1796812	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs1812589	0.81[ASN][1000 genomes]
rs1826978	0.82[ASN][1000 genomes]
rs1908089	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2028212	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2047435	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2131558	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2307077	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs34045364	0.82[ASN][1000 genomes]
rs34177389	0.82[ASN][1000 genomes]
rs34486572	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34984955	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35290302	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35591768	0.82[ASN][1000 genomes]
rs35837767	0.81[ASN][1000 genomes]
rs36054685	0.86[ASN][1000 genomes]
rs3737574	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3765682	0.86[JPT][hapmap]
rs3795251	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs3819949	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs4949884	0.82[ASN][1000 genomes]
rs5019550	0.82[ASN][1000 genomes]
rs56350137	0.82[ASN][1000 genomes]
rs5745314	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5745327	0.81[JPT][hapmap]
rs5745334	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5745343	0.81[JPT][hapmap]
rs5745353	0.88[ASN][1000 genomes]
rs5745392	0.81[JPT][hapmap]
rs5745426	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5745429	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5745451	0.90[JPT][hapmap]
rs5745464	0.80[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs5745465	0.86[JPT][hapmap]
rs5745523	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs5745532	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs5745542	0.81[JPT][hapmap]
rs5745546	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs58552356	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61676733	0.82[ASN][1000 genomes]
rs6593520	0.80[GIH][hapmap]
rs6668963	0.81[ASN][1000 genomes]
rs6680389	0.81[ASN][1000 genomes]
rs6687882	0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs6695055	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs67108483	0.81[ASN][1000 genomes]
rs71656856	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7514912	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7516477	0.80[JPT][hapmap]
rs7525919	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7545057	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7548391	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7548991	0.91[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs9660848	0.91[CHB][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	esv1850335	chr1:76344705-76379497	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5745448	ACADM	cis	parietal	SCAN
rs5745448	ACADM	cis	cerebellum	SCAN
rs5745448	MSH4	cis	cerebellum	SCAN
rs5745448	MSH4	cis	parietal	SCAN

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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