Variant report

Variant	rs12040022
Chromosome Location	chr1:47587253-47587254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1021827	0.81[GIH][hapmap]
rs1039468	0.83[EUR][1000 genomes]
rs10890445	0.81[GIH][hapmap]
rs11211422	0.88[TSI][hapmap]
rs11211436	0.95[CEU][hapmap];0.95[CHB][hapmap]
rs11211441	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11211445	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12022219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026359	0.90[CEU][hapmap];0.89[TSI][hapmap]
rs12030385	0.80[EUR][1000 genomes]
rs12041262	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs12045381	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12140477	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140891	0.83[EUR][1000 genomes]
rs12141009	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap]
rs1502909	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap]
rs1553390	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs1847225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1988615	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2036462	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap]
rs4926728	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4926776	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55909645	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6682257	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72637973	0.89[EUR][1000 genomes]
rs9326151	0.81[GIH][hapmap]
rs9326152	0.81[GIH][hapmap]
rs9633412	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9633422	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9701888	0.94[CEU][hapmap];0.85[CHB][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	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv870705	chr1:47533705-47620126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871010	chr1:47533705-47637999	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv870899	chr1:47548974-47637999	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv945929	chr1:47578751-47617495	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12040022	SPATA6	cis	cerebellum	SCAN

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47587000-47595200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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