Variant report

Variant	rs2972408
Chromosome Location	chr5:42463609-42463610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10064323	0.91[ASN][1000 genomes]
rs10941576	0.91[ASN][1000 genomes]
rs10941577	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1117110	0.96[ASN][1000 genomes]
rs11738365	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11739243	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11741390	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11748084	0.88[EUR][1000 genomes]
rs12513643	0.89[ASN][1000 genomes]
rs12514403	0.85[JPT][hapmap]
rs12515480	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12517368	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12517931	0.89[ASN][1000 genomes]
rs12518010	0.95[ASN][1000 genomes]
rs12518274	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12520318	0.89[ASN][1000 genomes]
rs12522222	0.95[ASN][1000 genomes]
rs12522421	0.95[ASN][1000 genomes]
rs12523537	0.91[ASN][1000 genomes]
rs12654242	0.87[ASN][1000 genomes]
rs13153388	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13166255	0.81[ASN][1000 genomes]
rs13166285	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13169289	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13178282	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13178652	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13185872	0.91[ASN][1000 genomes]
rs13189275	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1396768	0.96[ASN][1000 genomes]
rs1396775	0.91[ASN][1000 genomes]
rs1472947	0.91[ASN][1000 genomes]
rs1509455	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1509456	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1509460	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1509462	1.00[JPT][hapmap]
rs1605851	0.93[ASN][1000 genomes]
rs16872537	0.89[ASN][1000 genomes]
rs16872543	0.89[ASN][1000 genomes]
rs16872564	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1858136	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1858138	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1876790	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1960498	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1979994	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2036745	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2089645	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2202883	0.96[ASN][1000 genomes]
rs2221712	0.96[ASN][1000 genomes]
rs2395970	0.96[ASN][1000 genomes]
rs28498583	0.95[ASN][1000 genomes]
rs28943877	0.89[ASN][1000 genomes]
rs28943879	0.86[ASN][1000 genomes]
rs2940912	0.87[ASN][1000 genomes]
rs2940913	0.93[CEU][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2940914	0.96[ASN][1000 genomes]
rs2940917	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2940918	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2940919	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2940922	0.98[ASN][1000 genomes]
rs2940923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940927	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2940934	0.96[ASN][1000 genomes]
rs2940937	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2940940	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2940944	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2940945	0.93[ASN][1000 genomes]
rs2972393	0.85[CEU][hapmap]
rs2972394	0.91[ASN][1000 genomes]
rs2972406	0.96[ASN][1000 genomes]
rs2972407	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2972410	0.98[ASN][1000 genomes]
rs2972411	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2972412	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2972413	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2972414	0.85[ASN][1000 genomes]
rs2972418	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2972420	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33956936	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3764453	0.91[ASN][1000 genomes]
rs4130114	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4358532	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4509029	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4530764	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4866781	0.95[ASN][1000 genomes]
rs4866782	0.95[ASN][1000 genomes]
rs4866788	0.95[ASN][1000 genomes]
rs4866795	0.89[ASN][1000 genomes]
rs4866896	0.89[ASN][1000 genomes]
rs4866901	0.89[ASN][1000 genomes]
rs4866919	0.95[ASN][1000 genomes]
rs4866931	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4866934	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6451621	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6451624	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6897318	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7705834	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7710528	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7721578	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7723304	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs906817	0.93[ASN][1000 genomes]
rs9686537	0.91[ASN][1000 genomes]
rs9687863	0.87[ASN][1000 genomes]
rs979233	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs991592	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42450000-42466800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:42454800-42471800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:42455000-42469600	Weak transcription	Lung	lung
4	chr5:42455000-42474400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:42455000-42477400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:42461600-42467000	Weak transcription	Fetal Stomach	stomach
7	chr5:42462000-42468200	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:42462000-42468400	Weak transcription	Adipose Nuclei	Adipose
9	chr5:42462000-42471600	Weak transcription	Fetal Intestine Large	intestine
10	chr5:42462000-42472000	Weak transcription	Fetal Lung	lung
11	chr5:42462200-42470000	Weak transcription	Left Ventricle	heart
12	chr5:42462200-42470400	Weak transcription	Fetal Intestine Small	intestine
13	chr5:42462200-42470800	Weak transcription	Aorta	Aorta
14	chr5:42462200-42470800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:42462200-42471000	Weak transcription	Ovary	ovary
16	chr5:42462200-42471600	Weak transcription	Psoas Muscle	Psoas
17	chr5:42462200-42472200	Weak transcription	Fetal Heart	heart
18	chr5:42463000-42467000	Weak transcription	Liver	Liver

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