Variant report

Variant	rs6546776
Chromosome Location	chr2:72805588-72805589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:72486307..72488161-chr2:72805384..72808002,2	K562	blood:
2	chr2:72798438..72800996-chr2:72804039..72807217,3	K562	blood:
3	chr2:72376084..72377923-chr2:72805455..72808072,2	K562	blood:
4	chr2:72802770..72805375-chr2:72805450..72807796,2	MCF-7	breast:

Extended variants
information (count: 158 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10183056	1.00[ASN][1000 genomes]
rs10186080	1.00[ASN][1000 genomes]
rs10190674	1.00[ASN][1000 genomes]
rs10203965	1.00[ASN][1000 genomes]
rs10206555	1.00[ASN][1000 genomes]
rs10211019	1.00[ASN][1000 genomes]
rs10460572	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496186	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865391	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865392	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126370	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126371	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126372	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126373	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126374	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126385	1.00[ASN][1000 genomes]
rs11684985	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894160	1.00[ASN][1000 genomes]
rs12052508	0.94[EUR][1000 genomes]
rs12471136	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476130	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476397	1.00[ASN][1000 genomes]
rs12618390	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713772	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713773	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713774	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989141	1.00[ASN][1000 genomes]
rs12996406	1.00[ASN][1000 genomes]
rs12998681	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008041	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008258	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13016873	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383535	1.00[ASN][1000 genomes]
rs13424607	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1396106	0.83[AMR][1000 genomes]
rs1400580	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400582	1.00[ASN][1000 genomes]
rs1446888	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446889	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446890	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446891	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446892	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446893	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446895	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568145	1.00[ASN][1000 genomes]
rs1711838	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992799	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995734	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2048171	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138683	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420565	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106879	1.00[ASN][1000 genomes]
rs3106880	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34127669	1.00[ASN][1000 genomes]
rs4144318	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407272	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852291	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852292	0.89[EUR][1000 genomes]
rs4852293	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852294	1.00[ASN][1000 genomes]
rs4852298	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852872	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852875	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852876	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852877	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852878	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852880	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852893	1.00[ASN][1000 genomes]
rs581976	1.00[ASN][1000 genomes]
rs583673	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585653	1.00[ASN][1000 genomes]
rs585938	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587431	1.00[ASN][1000 genomes]
rs597799	1.00[ASN][1000 genomes]
rs598547	1.00[ASN][1000 genomes]
rs602465	1.00[ASN][1000 genomes]
rs603324	1.00[ASN][1000 genomes]
rs613880	1.00[ASN][1000 genomes]
rs614653	1.00[ASN][1000 genomes]
rs619343	1.00[ASN][1000 genomes]
rs62149282	1.00[ASN][1000 genomes]
rs623095	1.00[ASN][1000 genomes]
rs625434	1.00[ASN][1000 genomes]
rs631550	1.00[ASN][1000 genomes]
rs632670	1.00[ASN][1000 genomes]
rs634476	1.00[ASN][1000 genomes]
rs634574	1.00[ASN][1000 genomes]
rs634785	1.00[ASN][1000 genomes]
rs634929	1.00[ASN][1000 genomes]
rs636319	1.00[ASN][1000 genomes]
rs636332	1.00[ASN][1000 genomes]
rs636734	1.00[ASN][1000 genomes]
rs641123	1.00[ASN][1000 genomes]
rs642847	1.00[ASN][1000 genomes]
rs645489	1.00[ASN][1000 genomes]
rs646357	1.00[ASN][1000 genomes]
rs647269	1.00[ASN][1000 genomes]
rs650352	1.00[ASN][1000 genomes]
rs653842	1.00[ASN][1000 genomes]
rs654157	1.00[ASN][1000 genomes]
rs6546765	1.00[ASN][1000 genomes]
rs6546777	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546778	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546779	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546782	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546783	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656370	1.00[ASN][1000 genomes]
rs656440	1.00[ASN][1000 genomes]
rs658067	1.00[ASN][1000 genomes]
rs661395	1.00[ASN][1000 genomes]
rs664652	1.00[ASN][1000 genomes]
rs666361	1.00[ASN][1000 genomes]
rs669074	1.00[ASN][1000 genomes]
rs6707435	1.00[ASN][1000 genomes]
rs6714580	1.00[ASN][1000 genomes]
rs671550	1.00[ASN][1000 genomes]
rs671721	1.00[ASN][1000 genomes]
rs6736305	1.00[ASN][1000 genomes]
rs6739002	1.00[ASN][1000 genomes]
rs6741956	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6742088	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742312	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747378	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674863	1.00[ASN][1000 genomes]
rs6750766	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761075	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs678684	1.00[ASN][1000 genomes]
rs680380	1.00[ASN][1000 genomes]
rs681574	1.00[ASN][1000 genomes]
rs681908	1.00[ASN][1000 genomes]
rs683328	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs684673	1.00[ASN][1000 genomes]
rs687325	1.00[ASN][1000 genomes]
rs687371	1.00[ASN][1000 genomes]
rs688433	1.00[ASN][1000 genomes]
rs7420391	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560529	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560599	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565198	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571064	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580268	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7588602	1.00[ASN][1000 genomes]
rs7591025	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591303	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592155	1.00[ASN][1000 genomes]
rs7598238	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601020	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601318	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603797	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983928	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990569	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1008335	chr2:72561463-72819704	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv582208	chr2:72690622-72835886	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv834257	chr2:72701083-72853548	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6546776	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72775000-72808800	Weak transcription	Ovary	ovary
2	chr2:72797200-72806800	Enhancers	A549	lung
3	chr2:72799600-72807400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:72800800-72806000	Weak transcription	Fetal Heart	heart
5	chr2:72802800-72806600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:72803000-72805600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:72804000-72807200	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:72804200-72806000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:72804200-72806800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:72804400-72819400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:72804600-72806200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:72804600-72806200	Weak transcription	HSMM	muscle
13	chr2:72805000-72806200	Weak transcription	Osteobl	bone
14	chr2:72805400-72806400	Enhancers	Placenta Amnion	Placenta Amnion

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