Variant report

Variant	rs1569158
Chromosome Location	chr2:151351927-151351928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10169336	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10497060	0.84[ASN][1000 genomes]
rs10803791	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930130	0.99[ASN][1000 genomes]
rs1108155	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11686078	0.85[ASN][1000 genomes]
rs12692718	1.00[ASN][1000 genomes]
rs12692720	1.00[ASN][1000 genomes]
rs12692722	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12692729	0.88[ASN][1000 genomes]
rs12692739	0.85[ASN][1000 genomes]
rs12692740	0.85[ASN][1000 genomes]
rs12692747	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12692748	0.88[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs13011082	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13011088	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13012155	1.00[ASN][1000 genomes]
rs13031372	0.87[ASN][1000 genomes]
rs1528431	0.81[CEU][hapmap]
rs1609302	0.95[ASN][1000 genomes]
rs1852688	0.96[ASN][1000 genomes]
rs1852689	0.99[ASN][1000 genomes]
rs1852690	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1919142	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2222760	0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2340852	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6432778	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6432779	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6432791	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6721757	0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6722263	0.96[ASN][1000 genomes]
rs6735265	0.96[ASN][1000 genomes]
rs6757626	0.85[ASN][1000 genomes]
rs72865991	0.84[ASN][1000 genomes]
rs7561737	1.00[ASN][1000 genomes]
rs7586782	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7600506	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7603369	0.88[ASN][1000 genomes]
rs7605020	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7609510	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv532473	chr2:151164210-151701860	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv834414	chr2:151209374-151413309	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1001777	chr2:151351927-151395620	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv2762286	chr2:151351927-151395632	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1569158	ORC4L	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151344000-151352000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:151344200-151352600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:151344400-151352000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:151344600-151352000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:151348200-151352200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:151349200-151352000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:151349200-151352200	Weak transcription	HSMMtube	muscle
8	chr2:151349200-151352400	Weak transcription	HUVEC	blood vessel
9	chr2:151350000-151352800	Enhancers	Osteobl	bone
10	chr2:151350600-151352000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:151350600-151352200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:151350600-151352200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:151350600-151352200	Enhancers	Hela-S3	cervix
14	chr2:151350600-151352800	Enhancers	NHDF-Ad	bronchial
15	chr2:151350600-151353000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:151350800-151352200	Enhancers	A549	lung
17	chr2:151350800-151352800	Enhancers	NHLF	lung
18	chr2:151351200-151352000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:151351200-151352200	Enhancers	HSMM	muscle
20	chr2:151351200-151352800	Enhancers	NHEK	skin
21	chr2:151351400-151352200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:151351400-151352400	Weak transcription	Fetal Lung	lung
23	chr2:151351400-151353400	Enhancers	Fetal Heart	heart
24	chr2:151351800-151352200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:151351800-151353400	Enhancers	HMEC	breast
26	chr2:151351800-151353600	Enhancers	NH-A	brain

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