Variant report

Variant	rs2283090
Chromosome Location	chr7:126720116-126720117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:126719826..126721988-chr7:126731679..126734281,2	K562	blood:
2	chr7:126718359..126720333-chr7:126729809..126731677,2	K562	blood:

Variant related genes	Relation type
ENSG00000179603	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1006728	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs10225883	0.80[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10252623	0.85[AMR][1000 genomes]
rs10954144	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11563708	1.00[JPT][hapmap]
rs11563717	1.00[JPT][hapmap]
rs11563719	0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11563728	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11760208	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1361954	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1361963	0.93[JPT][hapmap]
rs1419424	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1419446	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17863189	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17864136	1.00[JPT][hapmap]
rs17864137	1.00[JPT][hapmap]
rs17867755	1.00[ASN][1000 genomes]
rs1894731	1.00[CEU][hapmap];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]
rs2010184	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2237780	0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap]
rs2237784	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs2237786	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2237789	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2237790	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2237791	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2237792	1.00[JPT][hapmap]
rs2283091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2283092	1.00[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];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]
rs2283093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2283095	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2283096	1.00[JPT][hapmap]
rs2299525	0.87[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes]
rs2299530	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2299535	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2299537	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2299538	0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2299539	1.00[JPT][hapmap]
rs2299541	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3808122	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs3808126	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3808127	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4141410	0.93[JPT][hapmap]
rs6467105	0.85[AMR][1000 genomes]
rs6942923	1.00[CEU][hapmap];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]
rs6949620	1.00[JPT][hapmap]
rs6950012	0.80[AMR][1000 genomes]
rs6964926	0.86[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs6975798	0.93[JPT][hapmap]
rs6978939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6979287	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979572	0.94[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7778276	0.93[JPT][hapmap]
rs7778308	0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap]
rs7791539	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7792406	0.87[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs951111	0.87[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831121	chr7:126593363-126774413	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv889189	chr7:126699088-126963028	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2761367	chr7:126717157-126865324	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2283090	SND1	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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