Variant report

Variant	rs4461246
Chromosome Location	chr2:63027671-63027672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10153716	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1022110	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs11682530	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11688816	0.93[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11893131	1.00[CEU][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs12328837	0.93[JPT][hapmap]
rs12713467	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713468	0.96[CEU][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713469	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs12989754	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994674	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13013218	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13398408	0.96[YRI][hapmap]
rs13418889	0.82[EUR][1000 genomes]
rs1386399	0.87[JPT][hapmap]
rs1420018	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468748	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs1487074	0.93[JPT][hapmap]
rs1534418	0.87[JPT][hapmap]
rs1534420	0.87[JPT][hapmap]
rs1553832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17027429	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs1828398	0.96[CEU][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1872789	0.87[JPT][hapmap]
rs1872790	0.93[JPT][hapmap]
rs189671	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1906198	0.83[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs2058566	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]
rs2058567	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2080227	0.84[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2136737	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2204655	0.87[JPT][hapmap]
rs2204656	0.87[JPT][hapmap]
rs2215870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2421816	0.92[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2430388	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]
rs2539978	1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2539980	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2539985	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2539987	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs2710637	0.85[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2710638	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs2710639	0.88[CEU][hapmap]
rs2710640	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2710642	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2710647	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs34104251	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs360797	0.86[ASW][hapmap];0.88[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap]
rs360799	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs360800	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360801	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.88[ASN][1000 genomes]
rs360804	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs360807	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs360808	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs3927201	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671050	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671051	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4671448	0.90[CHB][hapmap]
rs4671450	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545968	0.93[JPT][hapmap]
rs6545969	0.93[JPT][hapmap]
rs6545971	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545972	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs6545973	0.92[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6705835	0.93[JPT][hapmap]
rs6757128	0.93[JPT][hapmap]
rs7557501	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs7562149	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.88[LWK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7562734	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7567923	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs7571916	0.84[EUR][1000 genomes]
rs7573756	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9678329	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9973612	0.92[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4461246	VPS54	cis	cerebellum	SCAN
rs4461246	HSPC159	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62982200-63033400	Weak transcription	Fetal Intestine Large	intestine
2	chr2:63010800-63032800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:63017000-63029000	Weak transcription	Ovary	ovary
4	chr2:63017000-63032600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:63017000-63033400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:63017000-63037400	Weak transcription	NHLF	lung
7	chr2:63017400-63032800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:63017400-63049400	Weak transcription	Fetal Heart	heart
9	chr2:63018200-63033400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:63019600-63043400	Weak transcription	Brain Angular Gyrus	brain
11	chr2:63020600-63082000	Weak transcription	Pancreas	Pancrea
12	chr2:63020800-63040200	Weak transcription	Left Ventricle	heart
13	chr2:63022200-63029000	Weak transcription	Osteobl	bone
14	chr2:63022400-63040400	Weak transcription	NHEK	skin
15	chr2:63022400-63041000	Weak transcription	HSMM	muscle
16	chr2:63022600-63029200	Weak transcription	Small Intestine	intestine
17	chr2:63022600-63031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:63022600-63032800	Weak transcription	Fetal Intestine Small	intestine
19	chr2:63022800-63028200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:63022800-63029000	Weak transcription	HMEC	breast
21	chr2:63022800-63032000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:63022800-63032800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:63022800-63032800	Weak transcription	Fetal Lung	lung
24	chr2:63022800-63033000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:63022800-63034400	Weak transcription	Primary B cells from cord blood	blood
26	chr2:63022800-63035800	Weak transcription	Fetal Kidney	kidney
27	chr2:63023400-63029200	Weak transcription	Adipose Nuclei	Adipose
28	chr2:63023800-63049000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:63024000-63032800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:63025000-63028000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:63025000-63028400	Weak transcription	NHDF-Ad	bronchial
32	chr2:63025200-63029200	Weak transcription	Stomach Mucosa	stomach
33	chr2:63026200-63029000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:63026200-63034200	Strong transcription	HepG2	liver
35	chr2:63026600-63027800	Enhancers	Dnd41	blood
36	chr2:63027000-63027800	Enhancers	Brain Anterior Caudate	brain
37	chr2:63027000-63028400	Genic enhancers	A549	lung
38	chr2:63027000-63028600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr2:63027200-63028000	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr2:63027200-63028600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:63027200-63029600	Enhancers	Liver	Liver
42	chr2:63027400-63027800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:63027400-63028000	Enhancers	Colon Smooth Muscle	Colon
44	chr2:63027400-63029000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:63027400-63029200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:63027400-63030000	Enhancers	GM12878-XiMat	blood
47	chr2:63027400-63032800	Weak transcription	Primary T cells from cord blood	blood

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