Variant report

Variant	rs1502908
Chromosome Location	chr1:47485891-47485892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1021827	0.84[CEU][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1021828	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10890443	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10890444	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10890445	0.84[CEU][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10890446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10890447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10890453	0.80[AMR][1000 genomes]
rs10890454	0.80[AMR][1000 genomes]
rs10890455	0.80[AMR][1000 genomes]
rs10890457	0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10890460	0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10890464	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1117514	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11211421	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11211422	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11211423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11211435	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11211439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs11211446	1.00[JPT][hapmap]
rs11211451	0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12022635	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12037014	0.97[GIH][hapmap];1.00[JPT][hapmap]
rs12404496	0.87[ASN][1000 genomes]
rs12564635	1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs12732488	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12734327	0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12736235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1393659	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1393667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1553391	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1827473	0.89[CEU][hapmap]
rs1827474	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1847222	0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1847223	1.00[JPT][hapmap]
rs1967757	0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2016160	1.00[JPT][hapmap]
rs2055500	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2134471	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2202219	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2405580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2405588	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4375314	0.80[AMR][1000 genomes]
rs4448558	1.00[JPT][hapmap]
rs4926773	0.80[AMR][1000 genomes]
rs4926785	0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4926793	0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs6664392	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs6664496	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6669621	0.80[AMR][1000 genomes]
rs6683137	0.80[AMR][1000 genomes]
rs6690005	0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7545399	0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs9326151	0.84[CEU][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9326152	0.83[CEU][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9326153	0.85[AMR][1000 genomes]
rs9659815	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9699932	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9701154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9701868	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9701886	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9701899	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9728169	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9729662	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9793202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs9793471	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9793711	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9793716	0.85[AMR][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1502908	MOBKL2C	cis	cerebellum	SCAN
rs1502908	GPBP1L1	cis	cerebellum	SCAN

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	chr1:47485400-47486200	Enhancers	Fetal Kidney	kidney

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