Variant report

Variant	rs10741099
Chromosome Location	chr10:18820341-18820342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10741100	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764566	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764584	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10828835	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10828859	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10828879	1.00[ASN][1000 genomes]
rs10828901	1.00[ASN][1000 genomes]
rs10828906	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10829038	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829133	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829139	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829140	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014830	1.00[ASN][1000 genomes]
rs11014852	1.00[ASN][1000 genomes]
rs11015243	0.81[EUR][1000 genomes]
rs11015263	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015306	0.84[EUR][1000 genomes]
rs11015307	0.84[EUR][1000 genomes]
rs11015411	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257556	0.85[EUR][1000 genomes]
rs12359508	1.00[ASN][1000 genomes]
rs12412484	0.81[EUR][1000 genomes]
rs12569760	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12570585	0.95[ASN][1000 genomes]
rs12765362	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771084	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12772534	1.00[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	1.00[ASN][1000 genomes]
rs1352655	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880682	0.84[EUR][1000 genomes]
rs1968961	0.84[EUR][1000 genomes]
rs2691159	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4328135	0.91[ASN][1000 genomes]
rs4578284	1.00[ASN][1000 genomes]
rs4747353	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4748474	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
rs4748480	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4748489	1.00[ASN][1000 genomes]
rs4748495	1.00[ASN][1000 genomes]
rs4748503	0.84[EUR][1000 genomes]
rs4748508	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482516	1.00[ASN][1000 genomes]
rs6482529	1.00[ASN][1000 genomes]
rs7068575	0.95[ASN][1000 genomes]
rs7070695	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071192	1.00[ASN][1000 genomes]
rs7071897	0.84[EUR][1000 genomes]
rs7073651	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7077692	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7078884	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7080903	1.00[ASN][1000 genomes]
rs7081811	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7082094	1.00[ASN][1000 genomes]
rs7084525	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085332	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7085587	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7086034	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7086911	0.91[ASN][1000 genomes]
rs7088214	0.95[ASN][1000 genomes]
rs7090293	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7091578	1.00[ASN][1000 genomes]
rs7095070	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098313	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099975	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101352	0.84[EUR][1000 genomes]
rs7895235	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907153	0.84[EUR][1000 genomes]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10741099	NSUN6	cis	Skin Sun Exposed Lower leg	GTEx
rs10741099	NSUN6	cis	Adipose Subcutaneous	GTEx
rs10741099	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10741099	RP11-499P20.2	cis	lung	GTEx
rs10741099	NSUN6	cis	Nerve Tibial	GTEx

Chromatin state (count:82 , 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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