Variant report

Variant	rs4933173
Chromosome Location	chr10:91846691-91846692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10159518	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160072	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160077	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160169	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736053	0.82[EUR][1000 genomes]
rs10736054	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10736055	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10736056	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748537	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785930	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10785938	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785939	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881718	1.00[CHB][hapmap]
rs12264971	0.90[EUR][1000 genomes]
rs1325734	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329164	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329165	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329166	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359549	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410899	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555825	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1575795	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1590823	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1813172	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854459	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887921	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964146	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2094121	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148024	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2419351	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2419364	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2419365	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2419366	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393229	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4590775	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4933167	1.00[CHB][hapmap]
rs4933172	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4933176	0.85[AFR][1000 genomes]
rs4933534	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4933535	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933539	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933541	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933545	0.88[EUR][1000 genomes]
rs4933546	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4933547	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583667	1.00[CHB][hapmap]
rs6583671	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6583681	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6583682	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6583685	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7070170	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7071916	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7072040	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7081098	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7081625	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7084327	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084467	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085546	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7097613	0.85[AFR][1000 genomes]
rs7097675	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7394365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7394397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750312	0.85[AFR][1000 genomes]
rs7897322	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7908376	0.85[AFR][1000 genomes]
rs7908608	0.85[AFR][1000 genomes]
rs9971108	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9971206	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043571	chr10:91568555-92036154	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv551874	chr10:91570211-92036154	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv949678	chr10:91589048-92016474	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv895883	chr10:91610601-92195828	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1039731	chr10:91645718-92198264	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv540743	chr10:91645718-92198264	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv467430	chr10:91681344-92297943	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv551875	chr10:91681344-92297943	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	esv1839881	chr10:91762226-91861413	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv519094	chr10:91769945-91927196	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4933173	CYP26C1	cis	parietal	SCAN
rs4933173	PCGF5	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91820000-91860000	Weak transcription	Primary B cells from cord blood	blood
2	chr10:91840600-91847000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:91846000-91846800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr10:91846400-91847200	Enhancers	H9 Cell Line	embryonic stem cell
5	chr10:91846400-91847200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:91846400-91847600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr10:91846400-91847600	Enhancers	NHLF	lung
8	chr10:91846400-91847800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr10:91846400-91848000	Enhancers	HMEC	breast
10	chr10:91846600-91846800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr10:91846600-91846800	Enhancers	GM12878-XiMat	blood
12	chr10:91846600-91847000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr10:91846600-91847000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr10:91846600-91847200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr10:91846600-91847200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr10:91846600-91847200	Enhancers	HUVEC	blood vessel
17	chr10:91846600-91847600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:91846600-91847600	Enhancers	Hela-S3	cervix
19	chr10:91846600-91847600	Enhancers	Osteobl	bone
20	chr10:91846600-91847800	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr10:91846600-91847800	Enhancers	NH-A	brain
22	chr10:91846600-91848000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:91846600-91848000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr10:91846600-91848000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr10:91846600-91848000	Enhancers	NHEK	skin
26	chr10:91846600-91848800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr10:91846600-91848800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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