Variant report

Variant	rs2058566
Chromosome Location	chr2:63179076-63179077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10173115	0.81[CHB][hapmap]
rs1022110	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11682530	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11688816	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11890276	0.81[CHB][hapmap]
rs11893131	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs12617178	0.80[MKK][hapmap]
rs12713467	0.86[ASN][1000 genomes]
rs12713468	0.87[CEU][hapmap];0.88[ASN][1000 genomes]
rs12713469	0.85[CHB][hapmap];0.94[CHD][hapmap]
rs12989754	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12994674	0.88[ASN][1000 genomes]
rs13013218	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13418889	0.84[EUR][1000 genomes]
rs1420018	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1468748	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs1553832	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17027429	0.96[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1828398	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs189671	0.82[ASN][1000 genomes]
rs2058567	0.91[EUR][1000 genomes]
rs2136737	0.82[ASN][1000 genomes]
rs2215870	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2421816	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2430388	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2539978	0.92[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs2539980	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2539985	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2539986	0.81[MKK][hapmap]
rs2539987	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs2710637	0.96[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs2710638	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2710639	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2710640	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710641	0.81[ASN][1000 genomes]
rs2710642	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710644	0.81[EUR][1000 genomes]
rs2710647	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs2710648	0.82[MKK][hapmap]
rs360799	0.81[ASN][1000 genomes]
rs360800	0.81[ASN][1000 genomes]
rs360801	0.81[ASN][1000 genomes]
rs360804	0.81[ASN][1000 genomes]
rs3927201	0.89[ASN][1000 genomes]
rs4461246	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671050	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs4671051	0.83[EUR][1000 genomes]
rs4671448	0.90[CHB][hapmap]
rs4671450	0.83[ASN][1000 genomes]
rs6545971	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545972	0.96[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs6545973	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6705798	0.96[CEU][hapmap];0.90[GIH][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs6739804	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs7557501	0.96[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs7562149	0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs7562734	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7567923	0.96[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs7571916	0.89[EUR][1000 genomes]
rs7573756	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs9678329	0.86[ASN][1000 genomes]
rs9789661	0.81[EUR][1000 genomes]
rs9973612	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	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
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2058566	VPS54	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63142400-63190800	Weak transcription	Brain Angular Gyrus	brain
2	chr2:63151200-63182800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:63151400-63194200	Weak transcription	Esophagus	oesophagus
4	chr2:63151400-63194200	Weak transcription	Fetal Brain Male	brain
5	chr2:63151400-63200800	Weak transcription	Fetal Stomach	stomach
6	chr2:63151400-63208800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:63154400-63209000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:63155400-63209000	Weak transcription	Psoas Muscle	Psoas
10	chr2:63157400-63188800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:63157400-63207400	Weak transcription	Pancreas	Pancrea
12	chr2:63160200-63190000	Weak transcription	Primary B cells from cord blood	blood
13	chr2:63161800-63184400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:63162000-63196800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:63162000-63199800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:63165200-63209200	Weak transcription	Aorta	Aorta
17	chr2:63167000-63194000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:63167400-63200800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:63167400-63206400	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:63167600-63181800	Weak transcription	HMEC	breast
21	chr2:63167600-63187400	Weak transcription	NHLF	lung
22	chr2:63167600-63206200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:63167600-63256000	Weak transcription	HSMMtube	muscle
24	chr2:63167800-63225800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:63168200-63220200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:63168400-63182600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:63168400-63187600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:63168800-63194000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:63169200-63181400	Strong transcription	HepG2	liver
30	chr2:63169200-63185000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:63169200-63206200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:63169200-63206600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:63169400-63179400	Strong transcription	NHDF-Ad	bronchial
34	chr2:63169400-63196400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:63169600-63180200	Strong transcription	Liver	Liver
36	chr2:63169600-63182600	Weak transcription	Placenta	Placenta
37	chr2:63169600-63182600	Weak transcription	Dnd41	blood
38	chr2:63169600-63228800	Weak transcription	GM12878-XiMat	blood
39	chr2:63169800-63206200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:63169800-63208600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:63169800-63237000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:63170200-63208000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:63170400-63206200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:63170400-63255600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:63170800-63185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:63171400-63209800	Weak transcription	Brain Anterior Caudate	brain
47	chr2:63171800-63208600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:63171800-63218600	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:63171800-63233000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:63172000-63182600	Weak transcription	Primary hematopoietic stem cells	blood

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