Variant report

Variant	rs12554849
Chromosome Location	chr9:72636743-72636744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10217790	0.82[ASN][1000 genomes]
rs1027282	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10511978	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10868348	0.87[ASN][1000 genomes]
rs11141101	0.87[ASN][1000 genomes]
rs11141106	0.89[ASN][1000 genomes]
rs11141122	0.89[ASN][1000 genomes]
rs11141246	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11141260	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11788010	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11789512	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790329	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336812	0.89[ASN][1000 genomes]
rs12353051	0.89[ASN][1000 genomes]
rs12353052	0.89[ASN][1000 genomes]
rs12551035	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12551904	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12552060	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12553082	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12554412	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12555905	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12683555	0.89[ASN][1000 genomes]
rs12683959	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12686422	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12686803	0.89[ASN][1000 genomes]
rs17442733	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17443354	0.89[ASN][1000 genomes]
rs17522643	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17522671	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131427	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2131428	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2172432	0.89[ASN][1000 genomes]
rs2201232	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2220736	0.88[ASN][1000 genomes]
rs2220737	0.89[ASN][1000 genomes]
rs4256644	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4397475	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4457397	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4458932	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55897975	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56200303	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56380265	0.89[ASN][1000 genomes]
rs56399669	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57388366	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61210535	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62572583	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62572585	0.89[ASN][1000 genomes]
rs62572586	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62572589	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62572598	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62572600	0.90[ASN][1000 genomes]
rs62572601	0.92[ASN][1000 genomes]
rs62572604	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62572605	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62572631	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62572633	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62572634	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66542913	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026012	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7026154	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72709193	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73456376	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954376	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs954378	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	nsv415477	chr9:72629228-72637760	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72634800-72637200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:72634800-72637200	Enhancers	Fetal Lung	lung
3	chr9:72634800-72637400	Enhancers	NHEK	skin
4	chr9:72634800-72637600	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr9:72634800-72637600	Enhancers	HMEC	breast
6	chr9:72635200-72636800	Enhancers	NHDF-Ad	bronchial
7	chr9:72635200-72637200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:72635200-72637200	Enhancers	NHLF	lung
9	chr9:72635200-72637600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr9:72635200-72637600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr9:72635200-72637600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:72635200-72637600	Enhancers	Brain Germinal Matrix	brain
13	chr9:72635400-72636800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:72635400-72637200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:72635400-72637200	Enhancers	HSMM	muscle
16	chr9:72635400-72637200	Enhancers	Osteobl	bone
17	chr9:72635400-72640000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:72635600-72636800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:72635600-72637000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:72635600-72638800	Weak transcription	Pancreas	Pancrea
21	chr9:72635800-72636800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:72635800-72637200	Enhancers	Brain Hippocampus Middle	brain
23	chr9:72635800-72637200	Enhancers	HUVEC	blood vessel
24	chr9:72636000-72637000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:72636000-72637600	Enhancers	Brain Anterior Caudate	brain
26	chr9:72636000-72637600	Enhancers	NH-A	brain
27	chr9:72636200-72637200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:72636400-72637000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:72636400-72637400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:72636600-72637600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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