Variant report

Variant	rs57579336
Chromosome Location	chr10:18862380-18862381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 143 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10400076	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10430567	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1055116	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10734063	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10741091	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10741111	0.94[ASN][1000 genomes]
rs10741115	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10741129	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10741132	0.88[AMR][1000 genomes]
rs10764582	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10764583	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10764600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10764601	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10764602	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10764603	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10764604	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10764605	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10764625	0.97[ASN][1000 genomes]
rs10764640	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10764691	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10828851	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10828870	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10828871	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10828872	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10828896	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10828911	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10828965	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10828967	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10828975	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10828983	0.99[ASN][1000 genomes]
rs10828984	0.83[ASN][1000 genomes]
rs10828991	0.97[ASN][1000 genomes]
rs10829009	0.97[ASN][1000 genomes]
rs10829022	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10829037	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10829039	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10829040	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10829058	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10829060	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10829070	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10829148	0.83[EUR][1000 genomes]
rs10829151	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10829213	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014892	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11014981	0.83[ASN][1000 genomes]
rs11015048	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11015077	0.99[ASN][1000 genomes]
rs11015105	0.83[ASN][1000 genomes]
rs11015196	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11015255	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11015312	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11015421	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11511084	0.84[ASN][1000 genomes]
rs11525266	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11593617	0.92[ASN][1000 genomes]
rs11812341	0.90[ASN][1000 genomes]
rs11815228	0.92[ASN][1000 genomes]
rs12219183	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12359758	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12569474	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12569487	0.87[AFR][1000 genomes]
rs12765238	0.83[ASN][1000 genomes]
rs12766105	0.92[ASN][1000 genomes]
rs12766314	0.81[ASN][1000 genomes]
rs12770851	0.82[ASN][1000 genomes]
rs12772009	0.81[ASN][1000 genomes]
rs12772522	0.83[ASN][1000 genomes]
rs12775419	0.83[ASN][1000 genomes]
rs12779694	0.83[ASN][1000 genomes]
rs12785031	0.88[ASN][1000 genomes]
rs2272274	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34237250	0.81[ASN][1000 genomes]
rs3740102	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817494	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4445544	0.92[ASN][1000 genomes]
rs4747349	0.82[AMR][1000 genomes]
rs4747350	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4748488	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748490	0.84[ASN][1000 genomes]
rs4748492	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748497	0.84[ASN][1000 genomes]
rs4748509	0.86[AMR][1000 genomes]
rs5022622	0.97[ASN][1000 genomes]
rs56410858	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57066269	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62634837	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62634838	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62636218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482533	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6482597	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7071300	0.83[ASN][1000 genomes]
rs7074644	0.83[ASN][1000 genomes]
rs7075135	0.83[ASN][1000 genomes]
rs7077722	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079325	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7081461	0.94[ASN][1000 genomes]
rs7081690	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7081977	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7085318	0.92[ASN][1000 genomes]
rs7086757	0.83[ASN][1000 genomes]
rs7087030	0.91[AMR][1000 genomes]
rs7088091	0.81[AMR][1000 genomes]
rs7093454	0.92[ASN][1000 genomes]
rs7099260	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7100880	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72787951	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs72787963	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7477076	0.96[ASN][1000 genomes]
rs7894016	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7895784	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7898781	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7899017	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7901598	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7904016	0.83[ASN][1000 genomes]
rs7904263	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7905365	0.83[ASN][1000 genomes]
rs7907891	0.92[ASN][1000 genomes]
rs7909570	0.87[AMR][1000 genomes]
rs7909845	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7917584	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7919487	0.92[ASN][1000 genomes]
rs7922550	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7922829	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7923480	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	esv34545	chr10:18821185-18908294	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv1793653	chr10:18827828-18888369	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1794817	chr10:18827828-18888369	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv1811259	chr10:18827828-18888369	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	esv1840241	chr10:18827828-18888369	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv1841068	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	esv1851495	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	esv1835982	chr10:18833550-18872699	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2757371	chr10:18835325-18906507	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv2759736	chr10:18835325-18906507	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv466760	chr10:18839350-18905935	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv550044	chr10:18839350-18905935	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv18824	chr10:18841137-18862749	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
15	nsv550056	chr10:18841795-18862728	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
16	esv1845973	chr10:18841795-18872699	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	esv1793359	chr10:18841795-18872872	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	esv20509	chr10:18852387-18862559	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	inside rSNPs	diseases
19	esv1801825	chr10:18853581-18872699	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs57579336	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs57579336	ARL5B	cis	multi-tissue	Pritchard
rs57579336	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs57579336	NSUN6	cis	lung	GTEx
rs57579336	RP11-499P20.2	cis	lung	GTEx
rs57579336	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs57579336	RP11-499P20.2	cis	Whole Blood	GTEx
rs57579336	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs57579336	ARL5B	cis	Whole Blood	GTEx
rs57579336	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs57579336	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs57579336	RP11-499P20.2	cis	Thyroid	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18840800-18867200	Weak transcription	Fetal Thymus	thymus
2	chr10:18842000-18866800	Weak transcription	Left Ventricle	heart
3	chr10:18842000-18868400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:18842000-18869200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:18842000-18886400	Weak transcription	Colon Smooth Muscle	Colon
6	chr10:18844000-18871000	Weak transcription	Fetal Heart	heart
7	chr10:18846200-18899200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:18846400-18866600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:18846600-18866600	Weak transcription	Pancreas	Pancrea
10	chr10:18848400-18915800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr10:18848800-18866800	Weak transcription	Aorta	Aorta
12	chr10:18849000-18868600	Weak transcription	Gastric	stomach
13	chr10:18849400-18866200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:18849800-18910800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr10:18850000-18865600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:18852600-18864800	Weak transcription	Ovary	ovary
17	chr10:18853200-18866800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr10:18858000-18863200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
19	chr10:18859600-18868600	Weak transcription	K562	blood
20	chr10:18860000-18863200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr10:18860400-18863200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr10:18861000-18862400	ZNF genes & repeats	Primary T cells from cord blood	blood
23	chr10:18861000-18862400	ZNF genes & repeats	Liver	Liver
24	chr10:18861000-18883200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr10:18861200-18862400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr10:18861400-18864000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
27	chr10:18861600-18862400	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr10:18861600-18866200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr10:18861600-18867000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr10:18861800-18863400	ZNF genes & repeats	Brain Germinal Matrix	brain
31	chr10:18861800-18869000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr10:18862000-18862400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:18862000-18866200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr10:18862200-18862400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr10:18862200-18862400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
36	chr10:18862200-18863400	Weak transcription	Primary B cells from cord blood	blood
37	chr10:18862200-18863400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:18862200-18865600	Weak transcription	Adipose Nuclei	Adipose
39	chr10:18862200-18866800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:18862200-18868800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr10:18862200-18894600	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links