Variant report

Variant	rs2430388
Chromosome Location	chr2:63106784-63106785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10153716	0.81[AFR][1000 genomes]
rs1022110	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs11682530	0.86[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11688816	0.86[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[ASN][1000 genomes]
rs11893131	1.00[CEU][hapmap];0.84[YRI][hapmap];0.93[EUR][1000 genomes]
rs12713467	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12713468	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12713469	0.95[CHB][hapmap];0.94[CHD][hapmap]
rs12989754	0.93[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12994674	0.85[ASN][1000 genomes]
rs13013218	0.93[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13398408	0.91[YRI][hapmap]
rs13418889	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1420018	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1468748	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.84[LWK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs1553832	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17027429	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1828398	0.96[CEU][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs189671	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1906198	0.83[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap]
rs2058566	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]
rs2058567	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2080227	0.84[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs2136737	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2215870	0.85[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2421816	0.92[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs2430386	0.81[AFR][1000 genomes]
rs2539978	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2539980	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2539981	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2539982	0.83[AFR][1000 genomes]
rs2539985	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2539987	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs2710637	0.92[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs2710638	0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs2710639	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2710640	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710642	0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710647	0.88[CHD][hapmap]
rs360797	0.80[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap]
rs360799	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[YRI][hapmap]
rs360800	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs360801	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs360804	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs360807	0.80[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.92[YRI][hapmap]
rs360808	0.85[CHD][hapmap]
rs3927201	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4461246	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671050	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs4671051	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4671450	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6545971	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545972	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6545973	0.92[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs6705798	0.88[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap]
rs6739804	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap]
rs7557501	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7562149	0.93[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.86[LWK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]
rs7562734	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7567923	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7571916	0.87[EUR][1000 genomes]
rs7573756	0.80[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9678329	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9789661	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9973612	0.92[CEU][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2430388	VPS54	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63061200-63115200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:63098200-63108200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:63098400-63114400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:63099600-63112200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:63099800-63107400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:63100200-63107000	Strong transcription	HSMM	muscle
7	chr2:63100200-63108000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:63100800-63113400	Strong transcription	HepG2	liver
9	chr2:63101000-63107400	Strong transcription	NHDF-Ad	bronchial
10	chr2:63101000-63107600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:63101000-63110800	Strong transcription	Liver	Liver
12	chr2:63101000-63111200	Weak transcription	HUVEC	blood vessel
13	chr2:63101000-63111400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:63101000-63115000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:63101200-63110200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:63101400-63108000	Strong transcription	Adipose Nuclei	Adipose
17	chr2:63101400-63110800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:63101600-63107200	Strong transcription	NHLF	lung
19	chr2:63102200-63107200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr2:63102400-63108200	Strong transcription	A549	lung
21	chr2:63102400-63111200	Weak transcription	Hela-S3	cervix
22	chr2:63102400-63119000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:63102400-63146200	Weak transcription	Aorta	Aorta
24	chr2:63102600-63106800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:63102600-63108200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:63102600-63149800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:63102800-63111600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:63102800-63130600	Weak transcription	Fetal Intestine Small	intestine
29	chr2:63102800-63150200	Weak transcription	Esophagus	oesophagus
30	chr2:63103000-63107200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
31	chr2:63103000-63107400	Weak transcription	Brain Anterior Caudate	brain
32	chr2:63103200-63112000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:63103400-63112200	Weak transcription	Placenta	Placenta
34	chr2:63103400-63115800	Weak transcription	Small Intestine	intestine
35	chr2:63104000-63147800	Weak transcription	Fetal Stomach	stomach
36	chr2:63104200-63108200	Strong transcription	Dnd41	blood
37	chr2:63104200-63114600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:63104200-63126600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:63104400-63107000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:63104400-63107000	Weak transcription	NHEK	skin
41	chr2:63104400-63107800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:63104400-63108200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:63104400-63125000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:63104600-63106800	Weak transcription	Brain Substantia Nigra	brain
45	chr2:63104600-63107200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:63104600-63108600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:63104600-63110200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:63104600-63112000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr2:63104600-63112200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr2:63104600-63133200	Weak transcription	Colon Smooth Muscle	Colon

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