Variant report

Variant	rs56399669
Chromosome Location	chr9:72628517-72628518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10217790	0.88[ASN][1000 genomes]
rs1027282	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10511978	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10868348	0.93[ASN][1000 genomes]
rs11141101	0.93[ASN][1000 genomes]
rs11141106	0.95[ASN][1000 genomes]
rs11141122	0.95[ASN][1000 genomes]
rs11141127	0.80[ASN][1000 genomes]
rs11141246	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11141260	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11788010	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11789512	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11790329	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12336812	0.95[ASN][1000 genomes]
rs12353051	0.95[ASN][1000 genomes]
rs12353052	0.95[ASN][1000 genomes]
rs12551035	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12551904	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552060	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12553082	0.90[EUR][1000 genomes]
rs12554412	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12554849	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12555905	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12683555	0.95[ASN][1000 genomes]
rs12683959	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686422	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686803	0.95[ASN][1000 genomes]
rs17442733	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17443354	0.95[ASN][1000 genomes]
rs17522643	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17522671	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2131427	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2131428	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2172432	0.95[ASN][1000 genomes]
rs2201232	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2220736	0.94[ASN][1000 genomes]
rs2220737	0.95[ASN][1000 genomes]
rs4256644	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4397475	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4457397	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4458932	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs55897975	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56200303	0.90[EUR][1000 genomes]
rs56380265	0.95[ASN][1000 genomes]
rs57388366	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61210535	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62572583	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62572585	0.95[ASN][1000 genomes]
rs62572586	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62572589	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62572598	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62572600	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62572601	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62572604	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62572605	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62572631	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62572633	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62572634	0.90[EUR][1000 genomes]
rs66542913	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7026012	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7026154	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72709193	0.90[EUR][1000 genomes]
rs73456376	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs954376	0.90[EUR][1000 genomes]
rs954378	0.90[EUR][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	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv831612	chr9:72473778-72634253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1035668	chr9:72555053-72632796	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1051004	chr9:72557761-72632015	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72621200-72635400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72621400-72628800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:72625200-72628600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:72626000-72628600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:72626200-72629000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:72626200-72629200	Enhancers	HSMM	muscle
7	chr9:72626400-72629000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr9:72626400-72629200	Enhancers	NH-A	brain
9	chr9:72626600-72629200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr9:72626800-72629000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr9:72627000-72629200	Enhancers	Stomach Smooth Muscle	stomach
12	chr9:72627600-72629200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:72627600-72629200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:72627600-72629200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:72627600-72629200	Enhancers	HMEC	breast
16	chr9:72627800-72632600	Weak transcription	Ovary	ovary
17	chr9:72627800-72633200	Weak transcription	Fetal Lung	lung
18	chr9:72628000-72628800	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:72628200-72629000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:72628200-72629200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:72628200-72629200	Enhancers	NHDF-Ad	bronchial
22	chr9:72628200-72629200	Enhancers	NHEK	skin
23	chr9:72628200-72629200	Enhancers	NHLF	lung
24	chr9:72628200-72629400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:72628400-72628600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:72628400-72629000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:72628400-72629000	Enhancers	Brain Germinal Matrix	brain
28	chr9:72628400-72629000	Enhancers	Osteobl	bone
29	chr9:72628400-72629200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:72628400-72629200	Enhancers	HSMMtube	muscle

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