Variant report

Variant	rs57066269
Chromosome Location	chr10:18936646-18936647
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1055116	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10734063	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10741111	0.88[ASN][1000 genomes]
rs10741115	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10741129	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741132	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10764582	0.86[AMR][1000 genomes]
rs10764583	0.81[AMR][1000 genomes]
rs10764600	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10764601	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10764602	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10764603	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10764604	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10764605	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10764625	0.88[ASN][1000 genomes]
rs10764640	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10764691	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10828851	0.82[AMR][1000 genomes]
rs10828870	0.86[AMR][1000 genomes]
rs10828871	0.88[AMR][1000 genomes]
rs10828872	0.89[AMR][1000 genomes]
rs10828896	0.91[AMR][1000 genomes]
rs10828911	0.93[AMR][1000 genomes]
rs10828965	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10828975	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10828983	0.86[ASN][1000 genomes]
rs10828991	0.88[ASN][1000 genomes]
rs10829009	0.88[ASN][1000 genomes]
rs10829022	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10829037	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10829039	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10829040	0.89[AMR][1000 genomes]
rs10829058	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10829060	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10829070	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10829148	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10829151	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10829213	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11014892	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11015048	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11015077	0.86[ASN][1000 genomes]
rs11015196	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11015255	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11015312	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11015421	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11525266	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11540309	0.81[ASN][1000 genomes]
rs11812341	0.82[ASN][1000 genomes]
rs12219183	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12359758	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12569474	0.91[AMR][1000 genomes]
rs12762481	0.82[ASN][1000 genomes]
rs12780652	0.82[ASN][1000 genomes]
rs12785031	0.81[ASN][1000 genomes]
rs2272274	0.86[AMR][1000 genomes]
rs3740102	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3740104	0.81[ASN][1000 genomes]
rs3817494	0.81[AMR][1000 genomes]
rs4747350	0.82[AMR][1000 genomes]
rs4748488	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4748492	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4748497	0.84[ASN][1000 genomes]
rs4748509	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5022622	0.88[ASN][1000 genomes]
rs56410858	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57579336	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62634837	0.85[AMR][1000 genomes]
rs62634838	0.85[AMR][1000 genomes]
rs62636218	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6482533	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6482597	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7077722	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7079325	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7081461	0.86[ASN][1000 genomes]
rs7081690	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7081977	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7087030	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7099260	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7100880	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72787951	0.81[AMR][1000 genomes]
rs72787963	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7477076	0.88[ASN][1000 genomes]
rs7894016	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7895784	0.86[ASN][1000 genomes]
rs7898781	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7899017	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7901598	0.93[AMR][1000 genomes]
rs7904263	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7909570	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7909845	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7910902	0.85[ASN][1000 genomes]
rs7917584	0.84[AMR][1000 genomes]
rs7922550	0.81[AMR][1000 genomes]
rs7922829	0.81[AMR][1000 genomes]
rs7923480	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs57066269	RP11-499P20.2	cis	Whole Blood	GTEx
rs57066269	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs57066269	RP11-499P20.2	cis	Thyroid	GTEx
rs57066269	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs57066269	ARL5B	cis	Whole Blood	GTEx
rs57066269	NSUN6	cis	lung	GTEx
rs57066269	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs57066269	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs57066269	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs57066269	ARL5B	cis	multi-tissue	Pritchard
rs57066269	RP11-499P20.2	cis	lung	GTEx
rs57066269	RP11-499P20.2	cis	Nerve Tibial	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18905000-18938200	Weak transcription	Hela-S3	cervix
2	chr10:18916800-18937000	Weak transcription	GM12878-XiMat	blood
3	chr10:18916800-18938400	Weak transcription	HSMMtube	muscle
4	chr10:18916800-18939800	Weak transcription	Aorta	Aorta
5	chr10:18916800-18940200	Weak transcription	Spleen	Spleen
6	chr10:18917000-18936800	Weak transcription	Brain Germinal Matrix	brain
7	chr10:18917000-18937200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr10:18917000-18937400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr10:18917000-18938000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr10:18917000-18938200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr10:18917000-18938200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:18917000-18938200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr10:18917000-18938200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:18917000-18938200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:18917000-18938200	Weak transcription	Brain Angular Gyrus	brain
16	chr10:18917000-18938400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr10:18917000-18938400	Weak transcription	Ovary	ovary
18	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr10:18917000-18938800	Weak transcription	HSMM	muscle
21	chr10:18917000-18939600	Weak transcription	Placenta	Placenta
22	chr10:18917000-18939800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr10:18917000-18940200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:18917000-18940200	Weak transcription	Lung	lung
25	chr10:18917200-18937800	Weak transcription	Adipose Nuclei	Adipose
26	chr10:18921400-18939000	Weak transcription	Right Ventricle	heart
27	chr10:18922600-18939600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr10:18924800-18937800	Weak transcription	Fetal Lung	lung
29	chr10:18925200-18937600	Weak transcription	Fetal Heart	heart
30	chr10:18925200-18939200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr10:18925600-18939400	Weak transcription	Brain Substantia Nigra	brain
32	chr10:18926000-18940200	Weak transcription	Small Intestine	intestine
33	chr10:18926200-18939200	Weak transcription	Fetal Kidney	kidney
34	chr10:18926400-18938600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr10:18926600-18938200	Weak transcription	NHEK	skin
36	chr10:18927400-18939600	Weak transcription	Pancreas	Pancrea
37	chr10:18927800-18937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr10:18928000-18938400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:18928200-18938200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr10:18928200-18939400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr10:18928400-18938800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr10:18928800-18937800	Weak transcription	Brain Anterior Caudate	brain
43	chr10:18928800-18939600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr10:18928800-18939600	Weak transcription	Gastric	stomach
45	chr10:18929000-18937000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr10:18929000-18939000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr10:18929400-18936800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:18929600-18937200	Weak transcription	HepG2	liver
49	chr10:18929600-18938800	Weak transcription	Fetal Intestine Large	intestine
50	chr10:18930800-18937800	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links