Variant report

Variant	rs2861641
Chromosome Location	chr2:67794795-67794796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10490719	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10490720	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10490721	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1107595	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11126137	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11126139	0.91[ASN][1000 genomes]
rs11126140	0.92[ASN][1000 genomes]
rs11679082	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11680000	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11680926	0.90[ASN][1000 genomes]
rs11686555	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11693956	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12328339	0.90[ASN][1000 genomes]
rs12616261	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619942	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12621286	0.91[ASN][1000 genomes]
rs12624204	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17033787	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17033788	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2270342	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270343	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270344	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270346	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270348	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2861643	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2861650	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2861651	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2861679	0.91[ASN][1000 genomes]
rs2861688	0.90[ASN][1000 genomes]
rs2861692	0.90[ASN][1000 genomes]
rs2861693	0.89[ASN][1000 genomes]
rs2861696	0.89[ASN][1000 genomes]
rs2861697	0.86[ASN][1000 genomes]
rs2861699	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2902020	0.89[ASN][1000 genomes]
rs3885079	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4233940	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4368311	0.91[ASN][1000 genomes]
rs4444509	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4591326	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4671185	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4671186	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671187	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671188	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4671189	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671193	0.84[ASN][1000 genomes]
rs4671808	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60735969	0.95[ASN][1000 genomes]
rs61004148	0.94[ASN][1000 genomes]
rs6546323	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs723712	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72621572	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72621573	0.90[ASN][1000 genomes]
rs72621574	0.90[ASN][1000 genomes]
rs9309400	0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2861641	C2orf86	cis	cerebellum	SCAN
rs2861641	VPS54	cis	cerebellum	SCAN
rs2861641	C2orf42	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67789400-67795000	Weak transcription	Fetal Lung	lung
2	chr2:67789800-67795800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:67790400-67794800	Enhancers	HSMM	muscle
4	chr2:67790400-67798600	Weak transcription	Pancreas	Pancrea
5	chr2:67790800-67795000	Enhancers	NHDF-Ad	bronchial
6	chr2:67790800-67795600	Enhancers	Osteobl	bone
7	chr2:67792000-67795200	Weak transcription	Fetal Heart	heart
8	chr2:67792600-67795400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:67792800-67795600	Enhancers	A549	lung
10	chr2:67793400-67795400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:67793400-67795400	Enhancers	NH-A	brain
12	chr2:67793600-67794800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:67793600-67799400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:67793800-67799600	Weak transcription	Psoas Muscle	Psoas
15	chr2:67793800-67800400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:67793800-67803000	Weak transcription	Fetal Stomach	stomach
17	chr2:67794400-67798200	Weak transcription	Stomach Mucosa	stomach
18	chr2:67794400-67798600	Weak transcription	Left Ventricle	heart
19	chr2:67794400-67798600	Weak transcription	NHLF	lung
20	chr2:67794600-67796200	Enhancers	Hela-S3	cervix
21	chr2:67794600-67799000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:67794600-67799400	Weak transcription	HSMMtube	muscle

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