Variant report

Variant	rs10741129
Chromosome Location	chr10:18966907-18966908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:18962456..18966517-chr10:18966877..18973376,6	K562	blood:
2	chr10:18963664..18965385-chr10:18966665..18968377,2	K562	blood:
3	chr10:18966816..18969348-chr10:18971030..18973085,3	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1027193	0.81[ASN][1000 genomes]
rs1055116	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734063	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10741111	0.84[ASN][1000 genomes]
rs10741115	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10741132	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10764582	0.82[AMR][1000 genomes]
rs10764600	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10764601	0.88[AMR][1000 genomes]
rs10764603	0.88[AMR][1000 genomes]
rs10764625	0.81[ASN][1000 genomes]
rs10764640	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10764691	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10828851	0.81[AMR][1000 genomes]
rs10828870	0.82[AMR][1000 genomes]
rs10828871	0.84[AMR][1000 genomes]
rs10828872	0.86[AMR][1000 genomes]
rs10828896	0.87[AMR][1000 genomes]
rs10828911	0.89[AMR][1000 genomes]
rs10828965	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10828975	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10828991	0.81[ASN][1000 genomes]
rs10829009	0.81[ASN][1000 genomes]
rs10829022	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10829037	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10829039	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10829040	0.86[AMR][1000 genomes]
rs10829058	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10829060	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10829070	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10829148	0.90[EUR][1000 genomes]
rs10829151	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10829213	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11014892	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11015048	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11015196	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11015255	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11015312	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11015421	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11525266	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11540309	0.91[ASN][1000 genomes]
rs11812501	0.82[ASN][1000 genomes]
rs12098599	0.84[ASN][1000 genomes]
rs12219183	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12359758	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12569474	0.87[AMR][1000 genomes]
rs12765026	0.84[ASN][1000 genomes]
rs12767046	0.82[ASN][1000 genomes]
rs12782882	0.81[ASN][1000 genomes]
rs2272274	0.82[AMR][1000 genomes]
rs3740102	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4310518	0.80[ASN][1000 genomes]
rs4747350	0.81[AMR][1000 genomes]
rs4748488	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4748492	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4748509	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5022622	0.81[ASN][1000 genomes]
rs57066269	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57579336	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62634837	0.81[AMR][1000 genomes]
rs62634838	0.81[AMR][1000 genomes]
rs62636218	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6482533	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6482597	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7077722	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7079325	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7081461	0.82[ASN][1000 genomes]
rs7081690	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7081977	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7087030	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7096923	0.80[ASN][1000 genomes]
rs7099260	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7100880	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72787963	0.88[AMR][1000 genomes]
rs7477076	0.81[ASN][1000 genomes]
rs7894016	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7896918	0.84[ASN][1000 genomes]
rs7898781	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7899017	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7901598	0.89[AMR][1000 genomes]
rs7904263	0.88[AMR][1000 genomes]
rs7909570	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7909845	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7910902	0.94[ASN][1000 genomes]
rs7917584	0.83[AMR][1000 genomes]
rs7922005	0.86[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
rs10741129	RP11-499P20.2	cis	Thyroid	GTEx
rs10741129	NSUN6	cis	lung	GTEx
rs10741129	ARL5B	cis	Whole Blood	GTEx
rs10741129	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs10741129	RP11-499P20.2	cis	Whole Blood	GTEx
rs10741129	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs10741129	ARL5B	cis	multi-tissue	Pritchard
rs10741129	RP11-499P20.2	cis	lung	GTEx
rs10741129	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs10741129	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs10741129	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs10741129	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:18951000-18967400	Weak transcription	Esophagus	oesophagus
4	chr10:18951000-18971800	Weak transcription	Spleen	Spleen
5	chr10:18951000-18976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:18951400-18973800	Weak transcription	Aorta	Aorta
7	chr10:18954400-18967200	Weak transcription	Gastric	stomach
8	chr10:18954400-18969200	Weak transcription	Right Ventricle	heart
9	chr10:18954400-18973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:18955000-18972600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:18955200-18967600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr10:18955400-18969200	Weak transcription	Brain Angular Gyrus	brain
13	chr10:18955600-18968000	Weak transcription	Brain Substantia Nigra	brain
14	chr10:18956000-18970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr10:18956000-18972200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:18956200-18973200	Weak transcription	Small Intestine	intestine
17	chr10:18956400-18967800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr10:18957400-18968400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr10:18957400-18971600	Weak transcription	Fetal Heart	heart
20	chr10:18957600-18967200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr10:18957600-18969600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr10:18957600-18971200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr10:18957800-18971000	Weak transcription	Brain Anterior Caudate	brain
24	chr10:18958000-18967800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr10:18958000-18967800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr10:18958000-18968400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr10:18958200-18969800	Weak transcription	NHEK	skin
28	chr10:18958200-18970000	Weak transcription	HSMMtube	muscle
29	chr10:18959000-18973600	Weak transcription	Left Ventricle	heart
30	chr10:18960000-18972400	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:18960200-18969800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr10:18960400-18970200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr10:18960800-18970200	Weak transcription	NHLF	lung
34	chr10:18960800-18973400	Weak transcription	Ovary	ovary
35	chr10:18961000-18970800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr10:18961000-18973600	Weak transcription	Thymus	Thymus
37	chr10:18961600-18971000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr10:18961800-18970200	Weak transcription	HMEC	breast
39	chr10:18962400-18967200	Strong transcription	NH-A	brain
40	chr10:18962400-18973600	Weak transcription	Fetal Intestine Small	intestine
41	chr10:18962400-18973600	Weak transcription	Fetal Stomach	stomach
42	chr10:18963200-18967400	Weak transcription	Hela-S3	cervix
43	chr10:18963200-18973400	Weak transcription	Pancreas	Pancrea
44	chr10:18963600-18967800	Weak transcription	Fetal Brain Male	brain
45	chr10:18963800-18970000	Weak transcription	NHDF-Ad	bronchial
46	chr10:18964000-18972200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr10:18964000-18973000	Weak transcription	Primary T cells from cord blood	blood
48	chr10:18964200-18973400	Weak transcription	Psoas Muscle	Psoas
49	chr10:18964600-18967600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr10:18964600-18967800	Weak transcription	K562	blood

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