Variant report

Variant	rs17354547
Chromosome Location	chr4:142390869-142390870
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10519602	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12501765	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506151	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12507564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12507887	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12508511	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12508590	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12509285	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12509822	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510810	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511786	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511918	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12511983	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13105639	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13111616	0.80[EUR][1000 genomes]
rs13113365	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13117984	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13119177	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13122574	0.80[EUR][1000 genomes]
rs13129076	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13130612	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13131082	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13133795	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13145587	0.80[EUR][1000 genomes]
rs13147873	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1357158	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1402811	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1402812	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1436510	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521760	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521765	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1521766	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1554477	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1581387	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1581388	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1581390	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1608019	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17007301	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17354568	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949667	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2090878	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2103007	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2103008	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2322181	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34132448	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34147541	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34585213	0.89[EUR][1000 genomes]
rs34761999	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34865075	0.80[EUR][1000 genomes]
rs34963107	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35114853	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35251884	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35486128	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35815487	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35881750	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35898699	0.88[EUR][1000 genomes]
rs36043837	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36073635	0.82[ASN][1000 genomes]
rs4530710	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4956295	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4956297	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4956380	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4956384	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4956389	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4956396	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4956399	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55726691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55912825	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56029027	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56051122	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56074428	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56140725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56155233	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60008610	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326572	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62326579	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62326617	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68056864	0.88[EUR][1000 genomes]
rs6810477	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6812950	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6816897	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6818965	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6825913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826356	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6829748	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6831141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837400	0.80[EUR][1000 genomes]
rs6838410	0.89[EUR][1000 genomes]
rs6842807	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6845550	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6852094	0.89[EUR][1000 genomes]
rs6858423	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7671408	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7677830	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7680917	0.81[AFR][1000 genomes]
rs9761396	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[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	nsv880172	chr4:142355535-142565089	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17354547	TBC1D9	cis	parietal	SCAN
rs17354547	ZNF330	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142385800-142407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:142390400-142391000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:142390400-142391000	Enhancers	Muscle Satellite Cultured Cells	--
4	chr4:142390600-142391200	Enhancers	Osteobl	bone
5	chr4:142390600-142394000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:142390800-142391000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:142390800-142404400	Weak transcription	Pancreas	Pancrea

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