Variant report

Variant	rs4562286
Chromosome Location	chr8:99792066-99792067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10447977	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10755896	0.95[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap]
rs10755897	0.95[MEX][hapmap];0.93[TSI][hapmap]
rs10955189	0.85[AMR][1000 genomes]
rs10955190	0.82[CHB][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11774463	0.95[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs11778767	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11780292	0.82[AMR][1000 genomes]
rs11780369	0.82[AMR][1000 genomes]
rs11780500	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12114834	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12541317	0.95[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12547297	0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs12549803	0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs12550783	0.84[ASW][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs12679734	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12680195	0.82[CHB][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs13269932	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes]
rs13275915	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes]
rs13279438	0.90[AMR][1000 genomes]
rs1447245	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs1476181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1961744	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2028975	0.81[EUR][1000 genomes]
rs2442010	0.92[EUR][1000 genomes]
rs2442011	0.84[EUR][1000 genomes]
rs2442012	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2442013	0.82[EUR][1000 genomes]
rs2442014	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442015	0.91[CEU][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs2515214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2515215	0.92[EUR][1000 genomes]
rs2515216	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2515219	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2515221	0.81[EUR][1000 genomes]
rs2515224	0.90[EUR][1000 genomes]
rs2922066	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2922073	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2922074	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2922075	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2922076	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2922078	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2922081	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2922082	0.86[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3019290	0.85[AMR][1000 genomes]
rs3019291	0.85[AMR][1000 genomes]
rs3019293	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34281206	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34366206	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34477118	0.82[AMR][1000 genomes]
rs34855977	0.89[AMR][1000 genomes]
rs35536167	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35798019	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35804297	0.82[ASN][1000 genomes]
rs35915594	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4131873	0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4255105	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4279561	0.82[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes]
rs4292660	0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs4304299	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4440607	0.90[AMR][1000 genomes]
rs4509292	0.89[YRI][hapmap]
rs4517094	0.82[CHB][hapmap];0.87[AMR][1000 genomes]
rs4541872	0.85[AMR][1000 genomes]
rs4549741	0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes]
rs4612309	0.87[AMR][1000 genomes]
rs4734410	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes]
rs4734417	0.82[AMR][1000 genomes]
rs4735568	0.84[ASW][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs4735569	0.94[YRI][hapmap]
rs4735570	0.83[ASW][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs4735571	0.88[AMR][1000 genomes]
rs4735574	0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes]
rs57034072	0.86[AMR][1000 genomes]
rs58321500	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62532565	0.86[AMR][1000 genomes]
rs62532577	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62532587	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62535408	0.81[AMR][1000 genomes]
rs62535410	0.84[AMR][1000 genomes]
rs62535412	0.86[AMR][1000 genomes]
rs6468643	0.80[ASN][1000 genomes]
rs6988087	0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs6992925	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap]
rs7818828	0.87[MEX][hapmap];0.83[TSI][hapmap]
rs7827435	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7838239	0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7845271	0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs9656842	0.93[TSI][hapmap];0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv891220	chr8:99681858-99867419	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv1025685	chr8:99706280-99826236	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv539691	chr8:99706280-99826236	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4562286	NCALD	cis	cerebellum	SCAN
rs4562286	RGS22	cis	cerebellum	SCAN
rs4562286	OSR2	cis	cerebellum	SCAN
rs4562286	STK3	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99741600-99794200	Weak transcription	Pancreas	Pancrea
2	chr8:99758600-99794200	Weak transcription	Lung	lung
3	chr8:99759200-99794400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr8:99759800-99793400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr8:99763800-99794200	Weak transcription	NHLF	lung
6	chr8:99766000-99793200	Weak transcription	Primary T cells from cord blood	blood
7	chr8:99773000-99793000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr8:99774600-99793000	Weak transcription	Osteobl	bone
9	chr8:99775200-99793000	Weak transcription	Brain Hippocampus Middle	brain
10	chr8:99775400-99792800	Weak transcription	Primary B cells from cord blood	blood
11	chr8:99775600-99796200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr8:99776600-99798600	Weak transcription	Fetal Heart	heart
13	chr8:99776800-99797800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr8:99777200-99793000	Weak transcription	HSMMtube	muscle
15	chr8:99778600-99796200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr8:99778800-99793200	Weak transcription	Small Intestine	intestine
17	chr8:99778800-99793400	Weak transcription	HSMM	muscle
18	chr8:99779000-99792600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr8:99779000-99792600	Weak transcription	Adipose Nuclei	Adipose
20	chr8:99779000-99792600	Weak transcription	NHDF-Ad	bronchial
21	chr8:99779000-99796400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr8:99779000-99796400	Weak transcription	Aorta	Aorta
23	chr8:99779000-99796400	Weak transcription	Fetal Lung	lung
24	chr8:99779200-99793000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr8:99779200-99793000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr8:99779200-99793000	Weak transcription	HMEC	breast
27	chr8:99779200-99793200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr8:99779200-99793200	Weak transcription	Colon Smooth Muscle	Colon
29	chr8:99779400-99796000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr8:99779400-99796200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr8:99781000-99794200	Weak transcription	Right Atrium	heart
32	chr8:99781400-99792800	Weak transcription	Liver	Liver
33	chr8:99782200-99793600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr8:99785000-99796600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr8:99785200-99793200	Weak transcription	Left Ventricle	heart
36	chr8:99785200-99796000	Weak transcription	Fetal Muscle Leg	muscle
37	chr8:99785200-99796200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:99785400-99793000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr8:99785800-99793200	Weak transcription	Placenta	Placenta
40	chr8:99786600-99794200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr8:99787800-99793000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr8:99787800-99793400	Weak transcription	Thymus	Thymus
43	chr8:99788000-99793200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr8:99788000-99793200	Weak transcription	Ovary	ovary
45	chr8:99788200-99792600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr8:99788600-99793200	Weak transcription	NHEK	skin
47	chr8:99789000-99792800	Weak transcription	K562	blood
48	chr8:99789600-99793200	Weak transcription	Fetal Intestine Large	intestine
49	chr8:99789600-99796000	Weak transcription	Fetal Intestine Small	intestine
50	chr8:99789800-99793200	Weak transcription	Psoas Muscle	Psoas

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