Variant report

Variant	rs7917584
Chromosome Location	chr10:18820848-18820849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NSUN6-3	chr10:18820778-18820890	ENSG00000225527.1

Extended variants
information (count: 114 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10400076	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10508562	0.81[JPT][hapmap]
rs10508563	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs1055116	0.82[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes]
rs10734063	0.86[AMR][1000 genomes]
rs10741091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10741101	0.84[ASN][1000 genomes]
rs10741111	0.89[JPT][hapmap]
rs10741115	0.92[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes]
rs10741127	0.82[CEU][hapmap]
rs10741129	0.83[AMR][1000 genomes]
rs10741132	0.84[AMR][1000 genomes]
rs10764578	0.94[ASN][1000 genomes]
rs10764582	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10764583	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10764600	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10764601	0.92[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10764603	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10764625	0.81[JPT][hapmap]
rs10764640	0.83[AMR][1000 genomes]
rs10764691	0.83[AMR][1000 genomes]
rs10828851	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10828870	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10828871	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10828872	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10828896	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10828911	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10828965	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10828975	0.87[CEU][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10829022	0.91[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10829037	0.87[AMR][1000 genomes]
rs10829039	0.88[AMR][1000 genomes]
rs10829058	0.91[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs10829060	0.86[AMR][1000 genomes]
rs10829070	0.87[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs10829151	0.92[CEU][hapmap];0.86[AMR][1000 genomes]
rs10829213	0.83[AMR][1000 genomes]
rs11014634	0.97[ASN][1000 genomes]
rs11014892	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11014981	0.80[JPT][hapmap]
rs11015048	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11015196	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11015255	0.81[AMR][1000 genomes]
rs11015312	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs11015421	0.86[AMR][1000 genomes]
rs11525266	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11540309	0.85[JPT][hapmap]
rs12219183	0.83[AMR][1000 genomes]
rs12359758	0.86[AMR][1000 genomes]
rs12569474	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12762481	0.80[JPT][hapmap]
rs12767923	0.81[JPT][hapmap]
rs12769425	0.81[JPT][hapmap]
rs12774593	0.89[JPT][hapmap]
rs12778035	0.81[JPT][hapmap]
rs12781208	0.80[JPT][hapmap]
rs12784387	0.81[JPT][hapmap]
rs12784986	0.80[JPT][hapmap]
rs2228645	0.85[JPT][hapmap]
rs2272274	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3740102	0.91[CEU][hapmap];0.80[JPT][hapmap];0.87[AMR][1000 genomes]
rs3740104	0.81[JPT][hapmap]
rs3817494	0.80[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4237349	0.81[JPT][hapmap]
rs4314963	0.90[JPT][hapmap]
rs4445544	0.85[JPT][hapmap]
rs4468242	0.80[JPT][hapmap]
rs4747349	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4747350	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4748481	0.89[JPT][hapmap]
rs4748482	0.82[ASN][1000 genomes]
rs4748483	0.80[CEU][hapmap]
rs4748488	0.96[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4748492	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4748496	0.81[JPT][hapmap]
rs4748499	0.81[JPT][hapmap]
rs4748509	0.82[AMR][1000 genomes]
rs56410858	0.81[AMR][1000 genomes]
rs57066269	0.84[AMR][1000 genomes]
rs57579336	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62634837	0.85[AMR][1000 genomes]
rs62634838	0.85[AMR][1000 genomes]
rs62636218	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6482515	0.85[JPT][hapmap]
rs6482533	0.91[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6482597	0.87[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs7072624	0.81[JPT][hapmap]
rs7072963	0.80[JPT][hapmap]
rs7077722	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7079325	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7081690	0.83[AMR][1000 genomes]
rs7081977	0.86[AMR][1000 genomes]
rs7087030	0.84[AMR][1000 genomes]
rs7088091	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7096923	0.80[JPT][hapmap]
rs7099260	0.91[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs7099423	0.81[JPT][hapmap]
rs7100880	0.85[JPT][hapmap]
rs72787951	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72787963	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7894016	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7895784	0.85[JPT][hapmap]
rs7898513	0.83[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs7898781	0.86[AMR][1000 genomes]
rs7899017	0.86[AMR][1000 genomes]
rs7901598	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7904263	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7909570	0.81[AMR][1000 genomes]
rs7909845	0.82[AMR][1000 genomes]
rs7922550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7922829	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7923480	0.85[JPT][hapmap]

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	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	nsv1042073	chr10:18806900-18838303	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7917584	ARL5B	cis	multi-tissue	Pritchard
rs7917584	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs7917584	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs7917584	NSUN6	cis	lung	GTEx
rs7917584	ARL5B	cis	Whole Blood	GTEx
rs7917584	RP11-499P20.2	cis	lung	GTEx
rs7917584	RP11-499P20.2	cis	Thyroid	GTEx
rs7917584	RP11-499P20.2	cis	Whole Blood	GTEx
rs7917584	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs7917584	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs7917584	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs7917584	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18792400-18825400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr10:18799800-18825200	Weak transcription	Colonic Mucosa	Colon
3	chr10:18800200-18826800	Weak transcription	Brain Substantia Nigra	brain
4	chr10:18800400-18827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:18802000-18825000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:18802600-18828000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:18802600-18828200	Weak transcription	Lung	lung
8	chr10:18807200-18826800	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:18807400-18828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:18808000-18828000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:18808400-18827000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr10:18808800-18825400	Weak transcription	Fetal Brain Female	brain
13	chr10:18809000-18824000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:18809000-18827000	Weak transcription	Small Intestine	intestine
15	chr10:18810400-18828000	Weak transcription	Brain Angular Gyrus	brain
16	chr10:18810600-18827000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:18810600-18828200	Weak transcription	Aorta	Aorta
18	chr10:18810800-18825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:18810800-18828000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr10:18811000-18825400	Weak transcription	Right Ventricle	heart
21	chr10:18811000-18826800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:18812400-18825200	Weak transcription	Brain Anterior Caudate	brain
23	chr10:18812400-18827000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr10:18812600-18823000	Weak transcription	Colon Smooth Muscle	Colon
25	chr10:18812800-18827000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:18814000-18828000	Weak transcription	Esophagus	oesophagus
27	chr10:18814600-18825200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:18814600-18827000	Weak transcription	Thymus	Thymus
29	chr10:18814800-18825200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr10:18814800-18825400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr10:18814800-18827600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr10:18815000-18826800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr10:18815200-18825400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:18815200-18843600	Weak transcription	A549	lung
35	chr10:18815800-18828000	Weak transcription	K562	blood
36	chr10:18816400-18830400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr10:18816400-18841800	Strong transcription	Liver	Liver
38	chr10:18816800-18829600	Weak transcription	HSMMtube	muscle
39	chr10:18817400-18821800	Weak transcription	Fetal Kidney	kidney
40	chr10:18817400-18829000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr10:18818000-18821800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr10:18818200-18824000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr10:18818200-18825800	Weak transcription	Psoas Muscle	Psoas
44	chr10:18818600-18824200	Weak transcription	Fetal Stomach	stomach
45	chr10:18818600-18825200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:18818600-18825200	Weak transcription	Pancreas	Pancrea
47	chr10:18818800-18828000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr10:18818800-18828400	Weak transcription	Fetal Thymus	thymus
49	chr10:18819000-18825400	Weak transcription	Brain Germinal Matrix	brain
50	chr10:18819200-18822200	Weak transcription	Rectal Mucosa Donor 29	rectum

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