Variant report

Variant	rs11003872
Chromosome Location	chr10:55590722-55590723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10509000	0.85[JPT][hapmap]
rs10740556	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs10763010	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10763011	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10825114	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs10825115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10825117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10825119	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10825122	0.85[JPT][hapmap]
rs10825123	0.85[JPT][hapmap]
rs10825130	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs10825132	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10825133	0.89[ASN][1000 genomes]
rs11003868	1.00[CHB][hapmap]
rs11003871	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]
rs11003873	0.85[JPT][hapmap]
rs11003874	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11003876	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs11003878	0.85[JPT][hapmap]
rs11003879	1.00[JPT][hapmap]
rs11003888	0.82[JPT][hapmap]
rs12263108	0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12268247	1.00[JPT][hapmap]
rs16937793	0.85[JPT][hapmap]
rs16937794	0.85[JPT][hapmap]
rs16937797	0.85[JPT][hapmap]
rs16937801	0.85[JPT][hapmap]
rs1807888	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1900415	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1900417	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1900418	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs1900419	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1900443	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs1900455	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4310525	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs4417175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4417176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4519000	0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4540756	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4935096	0.80[CEU][hapmap]
rs4935472	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4935473	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4935474	0.85[JPT][hapmap]
rs6481042	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7074365	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089209	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];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7358121	1.00[JPT][hapmap]
rs766868	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7914433	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7916446	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1847684	chr10:55371601-55638740	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1842975	chr10:55378668-55736655	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv949692	chr10:55502542-55893206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv895429	chr10:55564355-55736655	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11003872	DKK1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:55590400-55590800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr10:55590600-55590800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:55590600-55591000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr10:55590600-55591200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr10:55590600-55591200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr10:55590600-55591200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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