Variant report

Variant	rs1770882
Chromosome Location	chr1:76411549-76411550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1001160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs10873797	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161848	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161887	0.84[CEU][hapmap]
rs11588643	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs1159215	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap]
rs12130832	0.95[CEU][hapmap]
rs12138898	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12142247	0.95[CEU][hapmap]
rs1251533	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1251584	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1303870	0.84[CEU][hapmap]
rs1498311	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs1628063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1630302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1630587	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1689270	1.00[CEU][hapmap]
rs1770889	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1796795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1796810	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1796813	1.00[CEU][hapmap]
rs1796815	1.00[CEU][hapmap]
rs1796827	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1856791	1.00[CEU][hapmap]
rs1908089	0.84[CEU][hapmap]
rs2029682	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs2307077	0.82[YRI][hapmap]
rs5745325	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs5745331	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs5745347	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap]
rs5745383	1.00[CEU][hapmap]
rs5745394	1.00[CEU][hapmap]
rs5745430	1.00[CEU][hapmap]
rs5745523	0.84[CEU][hapmap]
rs5745543	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs5745545	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5745546	0.84[CEU][hapmap]
rs5745547	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6656501	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap]
rs721204	1.00[CHD][hapmap]
rs879268	0.81[CEU][hapmap];0.82[ASN][1000 genomes]

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	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1770882	SNORD45B	cis	parietal	SCAN
rs1770882	RABGGTB	cis	cerebellum	SCAN
rs1770882	PIGK	cis	parietal	SCAN
rs1770882	SNORD45B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76402800-76420000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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