Variant report

Variant	rs6546000
Chromosome Location	chr2:63581819-63581820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10169209	0.83[EUR][1000 genomes]
rs10169292	0.83[EUR][1000 genomes]
rs10209822	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11125965	0.82[EUR][1000 genomes]
rs11125967	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11684108	0.80[EUR][1000 genomes]
rs11686044	0.83[EUR][1000 genomes]
rs11691357	0.83[EUR][1000 genomes]
rs11691718	0.80[EUR][1000 genomes]
rs11883730	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11894445	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12612773	0.81[EUR][1000 genomes]
rs12618974	0.89[EUR][1000 genomes]
rs12623431	0.80[EUR][1000 genomes]
rs12713477	0.80[EUR][1000 genomes]
rs12992737	0.84[EUR][1000 genomes]
rs12994711	0.80[EUR][1000 genomes]
rs13011799	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1400686	0.81[EUR][1000 genomes]
rs1400687	0.81[EUR][1000 genomes]
rs1400688	0.81[EUR][1000 genomes]
rs1517401	0.80[EUR][1000 genomes]
rs1517402	0.81[EUR][1000 genomes]
rs1517404	0.81[EUR][1000 genomes]
rs1517405	0.80[EUR][1000 genomes]
rs1517409	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1568175	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1607206	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1607207	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1829261	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1922421	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2090479	0.80[EUR][1000 genomes]
rs2176416	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2176417	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2176418	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2292794	0.89[EUR][1000 genomes]
rs2292795	0.89[EUR][1000 genomes]
rs2421883	0.82[EUR][1000 genomes]
rs2421886	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2421887	0.89[EUR][1000 genomes]
rs2901580	0.89[EUR][1000 genomes]
rs4313961	0.83[EUR][1000 genomes]
rs4353635	0.83[EUR][1000 genomes]
rs4429457	0.83[EUR][1000 genomes]
rs4578846	0.83[EUR][1000 genomes]
rs4671471	0.80[EUR][1000 genomes]
rs4671472	0.80[EUR][1000 genomes]
rs4671474	0.80[EUR][1000 genomes]
rs4671475	0.80[EUR][1000 genomes]
rs4671476	0.80[EUR][1000 genomes]
rs4671479	0.81[EUR][1000 genomes]
rs4671480	0.81[EUR][1000 genomes]
rs4671481	0.81[EUR][1000 genomes]
rs4671482	0.83[EUR][1000 genomes]
rs4671483	0.82[EUR][1000 genomes]
rs4671484	0.83[EUR][1000 genomes]
rs4671485	0.83[EUR][1000 genomes]
rs4671487	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671488	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4671494	0.87[EUR][1000 genomes]
rs6545986	0.80[EUR][1000 genomes]
rs6545989	0.81[EUR][1000 genomes]
rs6545991	0.83[EUR][1000 genomes]
rs6545992	0.83[EUR][1000 genomes]
rs6545997	0.84[EUR][1000 genomes]
rs6546001	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6546002	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6704562	0.81[EUR][1000 genomes]
rs6705322	0.84[EUR][1000 genomes]
rs6706180	0.80[EUR][1000 genomes]
rs6706424	0.80[EUR][1000 genomes]
rs6708627	0.81[EUR][1000 genomes]
rs6708847	0.80[EUR][1000 genomes]
rs6711248	0.80[EUR][1000 genomes]
rs6714139	0.81[EUR][1000 genomes]
rs6714298	0.80[EUR][1000 genomes]
rs6717060	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6724044	0.80[EUR][1000 genomes]
rs6725694	0.80[EUR][1000 genomes]
rs6728844	0.83[EUR][1000 genomes]
rs6729132	0.80[EUR][1000 genomes]
rs6734468	0.80[EUR][1000 genomes]
rs6737820	0.80[EUR][1000 genomes]
rs6741817	0.87[EUR][1000 genomes]
rs6744720	0.80[EUR][1000 genomes]
rs6744815	0.86[EUR][1000 genomes]
rs6755183	0.80[EUR][1000 genomes]
rs6757463	0.83[EUR][1000 genomes]
rs6757487	0.84[EUR][1000 genomes]
rs7558796	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7558922	0.83[EUR][1000 genomes]
rs7559137	0.83[EUR][1000 genomes]
rs7561802	0.83[EUR][1000 genomes]
rs7567088	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7570649	0.81[EUR][1000 genomes]
rs7571697	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7582434	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7591562	0.80[EUR][1000 genomes]
rs7599736	0.83[EUR][1000 genomes]
rs7605113	0.81[EUR][1000 genomes]
rs908621	0.89[EUR][1000 genomes]
rs908622	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs932171	0.86[EUR][1000 genomes]
rs932172	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv535768	chr2:63413596-63631407	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv834241	chr2:63490262-63668205	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1014935	chr2:63545598-63599535	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1012628	chr2:63545598-63604859	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1013613	chr2:63545598-63606689	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6546000	WDPCP	cis	Adipose Subcutaneous	GTEx
rs6546000	MDH1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63567800-63585600	Weak transcription	Gastric	stomach
2	chr2:63572000-63583000	Weak transcription	Primary T cells from cord blood	blood
3	chr2:63572000-63624000	Weak transcription	Left Ventricle	heart
4	chr2:63572800-63597000	Weak transcription	Dnd41	blood
5	chr2:63576800-63584600	Weak transcription	Brain Angular Gyrus	brain
6	chr2:63578000-63583600	Weak transcription	Primary B cells from cord blood	blood
7	chr2:63578600-63582400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:63579800-63582200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:63580800-63582200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:63581000-63583800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:63581000-63596400	Weak transcription	Aorta	Aorta
12	chr2:63581400-63582400	Weak transcription	Adipose Nuclei	Adipose
13	chr2:63581400-63622000	Weak transcription	Ovary	ovary

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