Variant report

Variant	rs10890445
Chromosome Location	chr1:47486392-47486393
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1021827	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1021828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1039469	0.81[EUR][1000 genomes]
rs10890443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890444	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890446	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs10890457	0.92[MKK][hapmap]
rs10890460	0.92[MKK][hapmap]
rs10890464	0.89[MKK][hapmap]
rs1117514	0.85[AFR][1000 genomes]
rs11211422	0.86[GIH][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap]
rs11211423	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs11211439	0.82[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap]
rs11211451	0.92[MKK][hapmap]
rs12022635	0.82[GIH][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap]
rs12037014	0.92[MKK][hapmap]
rs12041262	0.89[GIH][hapmap]
rs12141009	0.89[GIH][hapmap]
rs12564635	0.82[GIH][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap]
rs12734327	0.92[MKK][hapmap]
rs12736235	0.82[GIH][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1393659	0.85[AFR][1000 genomes]
rs1393667	0.82[GIH][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1502908	0.84[CEU][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1502909	0.87[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1553390	0.89[GIH][hapmap]
rs1553391	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1827473	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs1827474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847222	0.80[MKK][hapmap];0.82[YRI][hapmap]
rs1847225	0.83[GIH][hapmap]
rs1963620	0.80[EUR][1000 genomes]
rs1967757	0.92[MKK][hapmap]
rs2036462	0.87[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2055500	0.89[YRI][hapmap]
rs4448558	0.86[YRI][hapmap]
rs4926785	0.83[MEX][hapmap];0.92[MKK][hapmap]
rs4926793	0.92[MKK][hapmap]
rs6664392	0.89[MKK][hapmap]
rs6690005	0.92[MKK][hapmap]
rs7545399	0.89[MKK][hapmap]
rs9326151	0.94[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];0.98[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]
rs9326152	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326153	0.85[AFR][1000 genomes]
rs9699932	0.85[AFR][1000 genomes]
rs9701154	0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9701899	0.85[AFR][1000 genomes]
rs9729662	0.85[AFR][1000 genomes]
rs9793202	0.82[GIH][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap]
rs9793471	0.83[MEX][hapmap]
rs9793711	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9793716	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871958	chr1:47350374-47517123	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1009338	chr1:47358532-47555253	Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv870695	chr1:47363893-47502714	Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv871288	chr1:47363893-47507808	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv871377	chr1:47363893-47517123	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv546166	chr1:47407739-47495605	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv870674	chr1:47416441-47517123	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv871717	chr1:47449486-47524264	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10890445	C1orf50	cis	parietal	SCAN
rs10890445	GPBP1L1	cis	cerebellum	SCAN
rs10890445	MOBKL2C	cis	cerebellum	SCAN
rs10890445	ZNF514	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47481000-47487200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:47484400-47487200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:47484400-47489000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:47484800-47487600	Enhancers	Aorta	Aorta
5	chr1:47485000-47486800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:47486200-47487200	Weak transcription	Adipose Nuclei	Adipose

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