Variant report

Variant	rs7922829
Chromosome Location	chr10:18817374-18817375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10400076	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10508562	0.86[JPT][hapmap]
rs10508563	0.85[JPT][hapmap]
rs1055116	0.84[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs10734063	0.82[AMR][1000 genomes]
rs10741091	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10741101	0.87[ASN][1000 genomes]
rs10741111	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10741115	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs10741127	0.84[CEU][hapmap];0.80[YRI][hapmap]
rs10741132	0.81[AMR][1000 genomes]
rs10764578	0.97[ASN][1000 genomes]
rs10764582	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10764583	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10764600	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10764601	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10764603	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10764625	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs10828851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10828870	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10828871	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10828872	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10828896	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10828911	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10828965	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10828975	0.88[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10829022	0.92[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10829037	0.89[CHB][hapmap];0.83[AMR][1000 genomes]
rs10829039	0.84[AMR][1000 genomes]
rs10829058	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs10829060	0.82[AMR][1000 genomes]
rs10829070	0.88[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs10829151	0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs11014634	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11014892	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014981	0.86[JPT][hapmap]
rs11015048	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11015196	0.84[AMR][1000 genomes]
rs11015312	0.92[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs11015421	0.82[AMR][1000 genomes]
rs11511084	0.85[JPT][hapmap]
rs11525266	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11540309	0.90[JPT][hapmap]
rs11815228	0.88[CHB][hapmap]
rs12359758	0.82[AMR][1000 genomes]
rs12569474	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12762481	0.85[JPT][hapmap]
rs12764398	0.82[ASN][1000 genomes]
rs12766105	0.85[JPT][hapmap]
rs12766314	0.85[JPT][hapmap]
rs12767923	0.86[JPT][hapmap]
rs12769425	0.86[JPT][hapmap]
rs12770851	0.81[JPT][hapmap]
rs12772522	0.85[JPT][hapmap]
rs12774593	0.80[CHB][hapmap];0.82[ASN][1000 genomes]
rs12778035	0.86[JPT][hapmap]
rs12781208	0.86[JPT][hapmap]
rs12784387	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs12784986	0.85[JPT][hapmap]
rs12785031	0.82[JPT][hapmap]
rs2228645	0.90[JPT][hapmap]
rs2272274	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3740102	0.92[CEU][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes]
rs3740104	0.86[JPT][hapmap]
rs3817494	0.82[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4237349	0.86[JPT][hapmap]
rs4310518	0.81[JPT][hapmap]
rs4314963	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4445544	0.90[JPT][hapmap]
rs4468242	0.85[JPT][hapmap]
rs4747349	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4747350	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4748481	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4748483	0.82[CEU][hapmap]
rs4748488	0.96[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4748492	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4748496	0.86[JPT][hapmap]
rs4748499	0.86[JPT][hapmap]
rs5022622	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs57066269	0.81[AMR][1000 genomes]
rs57579336	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62634837	0.81[AMR][1000 genomes]
rs62634838	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs62636218	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6482515	0.90[JPT][hapmap]
rs6482533	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6482597	0.88[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs7072624	0.86[JPT][hapmap]
rs7072963	0.85[JPT][hapmap]
rs7077722	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7079325	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7081461	0.85[JPT][hapmap]
rs7081977	0.82[AMR][1000 genomes]
rs7087030	0.81[AMR][1000 genomes]
rs7088091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7096923	0.85[JPT][hapmap]
rs7099260	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs7099423	0.86[JPT][hapmap]
rs7100880	0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs72787951	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72787963	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7894016	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7895784	0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs7898513	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7898781	0.82[AMR][1000 genomes]
rs7899017	0.82[AMR][1000 genomes]
rs7901598	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7904016	0.85[JPT][hapmap]
rs7904263	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7904949	0.85[JPT][hapmap]
rs7905365	0.85[JPT][hapmap]
rs7917584	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]
rs7922550	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[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
rs7922829	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs7922829	ARL5B	cis	Whole Blood	GTEx
rs7922829	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs7922829	ARL5B	cis	multi-tissue	Pritchard
rs7922829	RP11-499P20.2	cis	Thyroid	GTEx
rs7922829	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs7922829	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs7922829	RP11-499P20.2	cis	lung	GTEx
rs7922829	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs7922829	NSUN6	cis	lung	GTEx
rs7922829	RP11-499P20.2	cis	Whole Blood	GTEx
rs7922829	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18778600-18818200	Weak transcription	Fetal Intestine Small	intestine
2	chr10:18792400-18825400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr10:18794000-18818400	Weak transcription	Fetal Brain Male	brain
4	chr10:18799800-18825200	Weak transcription	Colonic Mucosa	Colon
5	chr10:18800200-18826800	Weak transcription	Brain Substantia Nigra	brain
6	chr10:18800400-18827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:18800800-18818800	Weak transcription	Brain Germinal Matrix	brain
8	chr10:18800800-18819400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr10:18801000-18818800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr10:18802000-18825000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:18802600-18828000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr10:18802600-18828200	Weak transcription	Lung	lung
13	chr10:18807200-18826800	Weak transcription	Brain Hippocampus Middle	brain
14	chr10:18807400-18828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr10:18807600-18818800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr10:18808000-18828000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:18808400-18827000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr10:18808800-18825400	Weak transcription	Fetal Brain Female	brain
19	chr10:18809000-18824000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:18809000-18827000	Weak transcription	Small Intestine	intestine
21	chr10:18809200-18819000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr10:18809800-18817800	Weak transcription	Fetal Stomach	stomach
23	chr10:18809800-18817800	Weak transcription	Pancreas	Pancrea
24	chr10:18810400-18818400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr10:18810400-18828000	Weak transcription	Brain Angular Gyrus	brain
26	chr10:18810600-18827000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr10:18810600-18828200	Weak transcription	Aorta	Aorta
28	chr10:18810800-18825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:18810800-18828000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr10:18811000-18817800	Weak transcription	Ovary	ovary
31	chr10:18811000-18817800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr10:18811000-18818200	Weak transcription	Left Ventricle	heart
33	chr10:18811000-18825400	Weak transcription	Right Ventricle	heart
34	chr10:18811000-18826800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr10:18811200-18818800	Weak transcription	Fetal Lung	lung
36	chr10:18811200-18819000	Weak transcription	Fetal Intestine Large	intestine
37	chr10:18812400-18825200	Weak transcription	Brain Anterior Caudate	brain
38	chr10:18812400-18827000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr10:18812600-18823000	Weak transcription	Colon Smooth Muscle	Colon
40	chr10:18812800-18827000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr10:18813000-18817800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr10:18814000-18828000	Weak transcription	Esophagus	oesophagus
43	chr10:18814600-18825200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr10:18814600-18827000	Weak transcription	Thymus	Thymus
45	chr10:18814800-18825200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr10:18814800-18825400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr10:18814800-18827600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr10:18815000-18818800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:18815000-18826800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr10:18815200-18819800	Weak transcription	Dnd41	blood

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