Variant report

Variant	rs12097041
Chromosome Location	chr1:179401503-179401504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10494520	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs10753191	0.90[JPT][hapmap]
rs10753192	0.83[ASN][1000 genomes]
rs10798662	0.80[ASN][1000 genomes]
rs10798665	0.87[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap]
rs10798670	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs10913731	0.82[ASN][1000 genomes]
rs10913732	0.81[ASN][1000 genomes]
rs10913733	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10913734	0.90[JPT][hapmap]
rs10913742	0.88[ASN][1000 genomes]
rs10913758	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913806	0.88[CHB][hapmap]
rs12047160	0.82[ASN][1000 genomes]
rs12066948	1.00[ASW][hapmap]
rs12073906	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12073970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12118625	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12120123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12130876	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs12131473	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12131475	1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs12134114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12138436	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs12138619	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12140299	0.87[ASN][1000 genomes]
rs12144580	0.82[ASN][1000 genomes]
rs12405133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12405321	1.00[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs12408349	1.00[CHB][hapmap]
rs12408477	0.88[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap]
rs12725126	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12736300	0.91[ASN][1000 genomes]
rs12740270	0.91[ASN][1000 genomes]
rs12740455	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs12745772	1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs12759446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1329276	0.88[CHB][hapmap]
rs13306731	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13374852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16854009	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs16854229	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs2274623	0.81[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs2274625	0.81[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs28508518	0.87[ASN][1000 genomes]
rs35954891	0.87[ASN][1000 genomes]
rs36068644	0.87[ASN][1000 genomes]
rs3753526	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs4077551	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4077552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[ASN][1000 genomes]
rs41315575	0.81[ASN][1000 genomes]
rs4133136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs4394601	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59334094	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs61822772	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61824395	0.81[ASN][1000 genomes]
rs61826054	0.87[ASN][1000 genomes]
rs61826055	0.87[ASN][1000 genomes]
rs6425537	0.82[ASN][1000 genomes]
rs6669967	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs71514854	0.87[ASN][1000 genomes]
rs9660720	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs975025	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	esv1819329	chr1:179371973-179442337	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv466217	chr1:179371973-179477921	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv548297	chr1:179371973-179477921	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv548298	chr1:179376896-179436288	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12097041	ABL2	cis	cerebellum	SCAN
rs12097041	FAM20B	cis	parietal	SCAN
rs12097041	TNR	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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