Variant report

Variant	rs17823746
Chromosome Location	chr20:24591028-24591029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12480522	0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12481129	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12481146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17250061	0.83[MEX][hapmap]
rs17250068	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1883923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887057	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2024608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2026566	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2179800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2892216	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4813523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813524	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4815282	0.95[CEU][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4815286	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815287	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815288	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815289	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815290	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815291	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55770994	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58949684	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036849	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036851	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036854	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6049811	0.80[MEX][hapmap]
rs60869925	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7268862	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73345329	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73345369	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73345393	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8118304	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24583200-24599800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr20:24584400-24612600	Weak transcription	Aorta	Aorta
3	chr20:24589400-24594000	Weak transcription	Primary T cells from cord blood	blood
4	chr20:24590000-24591200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr20:24590000-24592200	Enhancers	Brain Cingulate Gyrus	brain
6	chr20:24590000-24592400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr20:24590000-24592600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr20:24590200-24592000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr20:24590400-24591400	Enhancers	GM12878-XiMat	blood
10	chr20:24590400-24591600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr20:24590400-24591800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr20:24590400-24591800	Enhancers	HSMM	muscle
13	chr20:24590400-24592000	Enhancers	NH-A	brain
14	chr20:24590400-24592400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr20:24590400-24592600	Enhancers	HMEC	breast
16	chr20:24590600-24591200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr20:24590600-24591200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr20:24590600-24591200	Enhancers	Brain Anterior Caudate	brain
19	chr20:24590600-24591600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr20:24590800-24591400	Enhancers	Brain Hippocampus Middle	brain
21	chr20:24590800-24591600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr20:24590800-24591800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr20:24590800-24592000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr20:24590800-24592400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr20:24591000-24591600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr20:24591000-24591600	Enhancers	Brain Substantia Nigra	brain
27	chr20:24591000-24591800	Enhancers	H1 Cell Line	embryonic stem cell
28	chr20:24591000-24591800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr20:24591000-24592000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr20:24591000-24592200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr20:24591000-24592400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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