Variant report

Variant	rs6762371
Chromosome Location	chr3:51871405-51871406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs12631654	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12637540	1.00[CHB][hapmap]
rs12639503	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394812	0.82[CHB][hapmap]
rs1468019	0.82[CHB][hapmap]
rs1505404	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1857800	0.85[EUR][1000 genomes]
rs1983106	1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2007607	1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2089224	0.85[EUR][1000 genomes]
rs2102297	0.87[AFR][1000 genomes]
rs28451928	0.85[EUR][1000 genomes]
rs28481670	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280629	0.89[JPT][hapmap]
rs4522758	1.00[CHB][hapmap]
rs55804132	0.85[EUR][1000 genomes]
rs55894445	0.85[EUR][1000 genomes]
rs56204016	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56222927	0.85[EUR][1000 genomes]
rs56285190	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56662100	0.85[EUR][1000 genomes]
rs56998832	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57184058	0.85[EUR][1000 genomes]
rs57269235	0.85[EUR][1000 genomes]
rs57407585	0.85[EUR][1000 genomes]
rs58932899	0.84[AFR][1000 genomes]
rs59215394	0.85[EUR][1000 genomes]
rs60818362	0.85[EUR][1000 genomes]
rs61015325	0.85[EUR][1000 genomes]
rs6446041	0.87[AFR][1000 genomes]
rs6762083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763197	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6768073	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782139	0.85[EUR][1000 genomes]
rs6786848	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6795223	1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs6795953	0.85[EUR][1000 genomes]
rs6798175	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798914	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6802583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6805324	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6805941	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809548	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73834762	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73834763	0.85[EUR][1000 genomes]
rs73834764	0.85[EUR][1000 genomes]
rs73834765	0.85[EUR][1000 genomes]
rs73834766	0.85[EUR][1000 genomes]
rs73838706	0.85[EUR][1000 genomes]
rs73838710	0.85[EUR][1000 genomes]
rs73838711	0.85[EUR][1000 genomes]
rs7615151	0.86[ASW][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap]
rs7627992	0.85[EUR][1000 genomes]
rs7632944	1.00[CHB][hapmap]
rs7635409	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7639080	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7644969	1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs9815475	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs9826967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828077	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9836804	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840336	0.82[CHB][hapmap]
rs9840833	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9853511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9856660	0.84[AFR][1000 genomes]
rs9857964	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859656	1.00[CHB][hapmap]
rs986539	1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs9866552	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869265	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874046	0.89[JPT][hapmap];0.96[YRI][hapmap]
rs9874547	0.89[JPT][hapmap];0.97[YRI][hapmap]
rs9875459	0.89[JPT][hapmap]
rs9880623	1.00[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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv3416846	chr3:51781117-51888179	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
6	nsv1001350	chr3:51860817-51899966	Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6762371	CSF3	trans	brain	seeQTL

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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