Variant report

Variant	rs1689271
Chromosome Location	chr1:76392862-76392863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76392792..76394366-chr1:76397859..76400177,2	K562	blood:

Variant related genes	Relation type
ENSG00000154007	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1021462	0.91[JPT][hapmap]
rs1021464	0.85[ASN][1000 genomes]
rs10732724	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10873738	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs10873804	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10873863	0.88[CEU][hapmap]
rs11161602	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11161731	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11161852	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs11161887	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11162066	0.81[CHB][hapmap]
rs1144328	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs1144331	0.85[JPT][hapmap]
rs1144333	0.80[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1144337	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs1144342	0.85[JPT][hapmap]
rs1146647	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1146648	0.81[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs1146649	0.85[JPT][hapmap]
rs1146651	0.85[JPT][hapmap]
rs1146652	0.85[JPT][hapmap]
rs12021750	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12022506	0.82[ASN][1000 genomes]
rs12024645	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs12032051	0.82[CHB][hapmap]
rs12033058	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12044025	0.86[JPT][hapmap]
rs12044211	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs12064158	0.82[CHB][hapmap]
rs12076093	0.81[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs12090712	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12401729	0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs12402230	0.86[ASN][1000 genomes]
rs12407107	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs12409592	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs12410373	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1251272	0.81[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs1251274	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1251579	0.83[ASN][1000 genomes]
rs1251580	0.83[ASN][1000 genomes]
rs1251581	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1251587	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1251588	0.83[ASN][1000 genomes]
rs1251591	0.82[ASN][1000 genomes]
rs1251594	0.85[ASN][1000 genomes]
rs12567390	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12703	0.85[JPT][hapmap]
rs12732495	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1303870	0.91[JPT][hapmap];0.82[LWK][hapmap]
rs1438175	0.82[CHB][hapmap]
rs1498313	0.81[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap]
rs1586936	0.85[ASN][1000 genomes]
rs1603734	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1658739	0.87[CEU][hapmap]
rs17097681	0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs17097695	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs17649675	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs1796812	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1873894	0.84[ASN][1000 genomes]
rs1908089	0.90[JPT][hapmap]
rs2028212	0.84[ASN][1000 genomes]
rs2047435	0.81[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs2066213	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2307077	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs35290302	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs3737574	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs3765682	0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs3795251	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3819949	0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs4949681	0.81[ASN][1000 genomes]
rs5745314	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs5745327	0.85[JPT][hapmap]
rs5745334	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs5745343	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs5745354	0.84[CHD][hapmap];0.80[JPT][hapmap]
rs5745392	0.85[JPT][hapmap]
rs5745429	0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs5745448	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs5745451	0.81[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs5745464	0.81[JPT][hapmap]
rs5745465	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs5745523	0.95[JPT][hapmap];0.82[YRI][hapmap]
rs5745532	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs5745542	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs5745546	0.95[JPT][hapmap];0.86[YRI][hapmap]
rs6687882	0.86[JPT][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap]
rs6693002	0.80[ASN][1000 genomes]
rs7514912	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs7520312	0.82[ASN][1000 genomes]
rs7524665	0.85[ASN][1000 genomes]
rs7525919	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7545057	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7548391	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs931506	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1689271	ACADM	cis	cerebellum	SCAN
rs1689271	MSH4	cis	parietal	SCAN
rs1689271	SNORD45B	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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