Variant report

Variant	rs531780
Chromosome Location	chr1:216117840-216117841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10746460	1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap]
rs12140657	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1408960	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1575756	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs1934424	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs2576002	0.90[CHB][hapmap]
rs2764947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2764951	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4564111	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs479826	0.90[CHB][hapmap]
rs489857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs494350	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs519859	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs542423	0.90[CHB][hapmap]
rs547022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553986	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs559921	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs568336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs654702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687019	0.90[CHB][hapmap]
rs687693	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7544470	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs927744	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949671	chr1:215942740-216120815	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv832548	chr1:215987089-216175724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv428599	chr1:216086224-216267211	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs531780	SMYD2	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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