Variant report

Variant	rs10829040
Chromosome Location	chr10:18917047-18917048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1055116	0.87[AMR][1000 genomes]
rs10734063	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10741111	0.80[ASN][1000 genomes]
rs10741115	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10741129	0.86[AMR][1000 genomes]
rs10741132	0.84[AMR][1000 genomes]
rs10764582	0.81[AMR][1000 genomes]
rs10764600	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10764601	0.87[AMR][1000 genomes]
rs10764603	0.87[AMR][1000 genomes]
rs10764640	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10764691	0.83[AMR][1000 genomes]
rs10828870	0.81[AMR][1000 genomes]
rs10828871	0.83[AMR][1000 genomes]
rs10828872	0.84[AMR][1000 genomes]
rs10828896	0.86[AMR][1000 genomes]
rs10828911	0.88[AMR][1000 genomes]
rs10828965	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10828975	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10829022	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10829037	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10829039	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10829058	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10829060	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10829070	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10829151	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10829213	0.83[AMR][1000 genomes]
rs11014892	0.87[AMR][1000 genomes]
rs11015048	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11015196	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11015255	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11015312	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11015421	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11525266	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12219183	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12359758	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12569474	0.86[AMR][1000 genomes]
rs2272274	0.81[AMR][1000 genomes]
rs3740102	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4748488	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4748492	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4748509	0.82[AMR][1000 genomes]
rs56410858	0.81[AMR][1000 genomes]
rs57066269	0.89[AMR][1000 genomes]
rs57579336	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62636218	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6482533	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6482597	0.87[AMR][1000 genomes]
rs7077722	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7079325	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7081690	0.88[AMR][1000 genomes]
rs7081977	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7087030	0.87[AMR][1000 genomes]
rs7099260	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7100880	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs72787963	0.87[AMR][1000 genomes]
rs7894016	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7898781	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7899017	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7901598	0.88[AMR][1000 genomes]
rs7904263	0.87[AMR][1000 genomes]
rs7909570	0.83[AMR][1000 genomes]
rs7909845	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv982911	chr10:18911989-18931479	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv3380756	chr10:18912943-18923066	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3392789	chr10:18915321-18925576	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10829040	NSUN6	cis	lung	GTEx
rs10829040	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs10829040	RP11-499P20.2	cis	Thyroid	GTEx
rs10829040	RP11-499P20.2	cis	lung	GTEx
rs10829040	RP11-499P20.2	cis	Whole Blood	GTEx
rs10829040	RP11-499P20.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18905000-18938200	Weak transcription	Hela-S3	cervix
2	chr10:18916200-18917200	Active TSS	Liver	Liver
3	chr10:18916800-18930400	Weak transcription	Dnd41	blood
4	chr10:18916800-18935200	Weak transcription	K562	blood
5	chr10:18916800-18936200	Weak transcription	A549	lung
6	chr10:18916800-18937000	Weak transcription	GM12878-XiMat	blood
7	chr10:18916800-18938400	Weak transcription	HSMMtube	muscle
8	chr10:18916800-18939800	Weak transcription	Aorta	Aorta
9	chr10:18916800-18940200	Weak transcription	Spleen	Spleen
10	chr10:18917000-18917200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr10:18917000-18917200	Enhancers	Adipose Nuclei	Adipose
12	chr10:18917000-18917400	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr10:18917000-18925000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:18917000-18925000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr10:18917000-18925800	Weak transcription	Fetal Intestine Small	intestine
16	chr10:18917000-18926000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:18917000-18926200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:18917000-18926800	Weak transcription	Fetal Intestine Large	intestine
19	chr10:18917000-18929000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:18917000-18929200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:18917000-18930200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr10:18917000-18930200	Weak transcription	Fetal Stomach	stomach
23	chr10:18917000-18930400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr10:18917000-18930400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr10:18917000-18930400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:18917000-18930400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr10:18917000-18930400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr10:18917000-18930400	Weak transcription	Fetal Muscle Leg	muscle
29	chr10:18917000-18930600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr10:18917000-18930600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr10:18917000-18930600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr10:18917000-18930600	Weak transcription	Left Ventricle	heart
33	chr10:18917000-18930800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:18917000-18932400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr10:18917000-18932600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:18917000-18934200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:18917000-18934200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr10:18917000-18934400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr10:18917000-18934600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr10:18917000-18934600	Weak transcription	Fetal Brain Female	brain
41	chr10:18917000-18934800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr10:18917000-18934800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr10:18917000-18935000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:18917000-18935000	Weak transcription	Primary T cells from cord blood	blood
45	chr10:18917000-18936800	Weak transcription	Brain Germinal Matrix	brain
46	chr10:18917000-18937200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr10:18917000-18937400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr10:18917000-18938000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr10:18917000-18938200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr10:18917000-18938200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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