Variant report

Variant	rs17040600
Chromosome Location	chr2:50634612-50634613
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10048731	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1005431	0.83[MEX][hapmap]
rs10181522	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10182951	0.82[EUR][1000 genomes]
rs10184843	0.95[CEU][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap]
rs10188271	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10190857	0.82[EUR][1000 genomes]
rs10191195	0.84[CHB][hapmap]
rs10191261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10201390	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs10203960	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs10205311	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10209627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10210660	0.90[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10490228	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11125306	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12465784	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12467043	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12473243	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12475335	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12475464	1.00[CEU][hapmap]
rs12475979	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12476139	0.85[EUR][1000 genomes]
rs12613343	0.83[EUR][1000 genomes]
rs12619946	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12620045	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12713097	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12713098	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713100	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12994492	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs13005521	1.00[CEU][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs13014058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13014624	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13032292	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13032775	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13382506	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13390864	0.81[EUR][1000 genomes]
rs13392422	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs13396103	0.83[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13407013	0.82[EUR][1000 genomes]
rs13407657	0.86[GIH][hapmap];0.80[EUR][1000 genomes]
rs13407788	0.82[EUR][1000 genomes]
rs13421278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13430295	0.90[CEU][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap]
rs13430435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1402124	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs1402128	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs1520437	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1520438	0.83[EUR][1000 genomes]
rs1520439	0.88[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1520443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1520446	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1520449	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1533692	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17040569	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17040577	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17040640	0.82[EUR][1000 genomes]
rs1818714	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1818715	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs1818716	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs1851015	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2160443	0.82[EUR][1000 genomes]
rs2351517	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs34846571	0.82[EUR][1000 genomes]
rs4638832	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57564327	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6709416	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs6709865	0.85[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs6711307	0.85[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs6717441	0.81[EUR][1000 genomes]
rs6718809	0.81[EUR][1000 genomes]
rs6738086	0.83[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6743117	0.82[EUR][1000 genomes]
rs6743562	0.83[EUR][1000 genomes]
rs6743584	0.82[EUR][1000 genomes]
rs6744418	0.81[EUR][1000 genomes]
rs6747128	0.81[EUR][1000 genomes]
rs6747258	0.81[EUR][1000 genomes]
rs6756081	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6756219	0.85[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs6756479	0.81[EUR][1000 genomes]
rs7567375	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7581097	0.95[CEU][hapmap]
rs7585229	0.82[EUR][1000 genomes]
rs7585534	0.81[EUR][1000 genomes]
rs9309182	0.85[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs939402	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948548	chr2:50569117-50695100	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv933786	chr2:50628354-50780185	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17040600	MSRA	trans	lymphoblastoid	seeQTL
rs17040600	MCFD2	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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