Variant report

Variant	rs1945282
Chromosome Location	chr11:56371633-56371634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10501354	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs10736676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs10736677	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs10736678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10792038	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs10792039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs10792040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10792043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[ASN][1000 genomes]
rs10896480	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10896501	0.91[ASN][1000 genomes]
rs11228641	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11228673	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11228676	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11228684	1.00[ASN][1000 genomes]
rs11228686	1.00[ASN][1000 genomes]
rs11228687	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11228693	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11228694	0.94[ASN][1000 genomes]
rs11228698	0.94[ASN][1000 genomes]
rs11228701	0.94[ASN][1000 genomes]
rs11228706	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11228708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11228759	0.94[CHD][hapmap];0.91[JPT][hapmap]
rs11228760	0.94[CHD][hapmap];0.91[JPT][hapmap]
rs11228763	0.94[CHD][hapmap];0.91[JPT][hapmap]
rs11228769	0.90[JPT][hapmap]
rs12222989	0.94[ASN][1000 genomes]
rs12223492	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12418150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12418301	1.00[ASN][1000 genomes]
rs1397056	0.86[AMR][1000 genomes]
rs1473592	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1605924	1.00[ASN][1000 genomes]
rs17150739	0.88[ASN][1000 genomes]
rs1945196	0.88[ASN][1000 genomes]
rs1945206	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1945210	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1945261	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1945263	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2089703	0.86[AMR][1000 genomes]
rs2202932	1.00[ASN][1000 genomes]
rs2511143	0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs2865516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs33995115	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4500505	0.88[ASN][1000 genomes]
rs4939061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4939065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs4939066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs583216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs583589	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs584608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs588805	0.88[ASN][1000 genomes]
rs592744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs596212	0.85[ASN][1000 genomes]
rs597680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs600187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs611397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs614942	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61710550	0.94[ASN][1000 genomes]
rs628524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs637912	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs642630	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs643384	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs645351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs646286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs654634	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs655779	0.88[ASN][1000 genomes]
rs656565	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6591323	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs6591381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6591382	0.82[AMR][1000 genomes]
rs6591383	0.86[AMR][1000 genomes]
rs674431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs676901	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs688832	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7924528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs7939886	0.88[ASN][1000 genomes]

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	nsv1050024	chr11:55900482-56518943	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
2	nsv497854	chr11:55917298-56537994	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv468576	chr11:56299930-56420029	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv555099	chr11:56299930-56420029	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1037096	chr11:56332750-56380919	Enhancers Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3384407	chr11:56344917-56380827	Weak transcription Enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
7	esv3398628	chr11:56344934-56380760	Enhancers Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv982949	chr11:56361311-56395993	Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv971952	chr11:56361311-56452186	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv949349	chr11:56371633-56593610	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1945282	OR8J1	cis	cerebellum	SCAN
rs1945282	APLNR	cis	parietal	SCAN
rs1945282	MS4A3	cis	parietal	SCAN
rs1945282	OR5B2	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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