Variant report

Variant	rs7899017
Chromosome Location	chr10:18943906-18943907
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARL5B-1	chr10:18943545-18943952	ENSG00000246675
2	lnc-NSUN6-2	chr10:18943793-18944104	ENSG00000152487.5
3	lnc-NSUN6-2	chr10:18943480-18944104	ENSG00000152487.5
4	lnc-NSUN6-2	chr10:18943617-18944104	ENSG00000152487.5
5	lnc-NSUN6-2	chr10:18943782-18944104	ENSG00000152487.6

Extended variants
information (count: 99 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10400076	0.81[AMR][1000 genomes]
rs1055116	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10734063	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10741111	0.88[ASN][1000 genomes]
rs10741115	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10741129	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741132	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10764582	0.87[AMR][1000 genomes]
rs10764583	0.83[AMR][1000 genomes]
rs10764600	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10764601	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10764602	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10764603	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10764604	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10764605	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10764625	0.88[ASN][1000 genomes]
rs10764640	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10764691	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10828851	0.84[AMR][1000 genomes]
rs10828870	0.87[AMR][1000 genomes]
rs10828871	0.90[AMR][1000 genomes]
rs10828872	0.91[AMR][1000 genomes]
rs10828896	0.92[AMR][1000 genomes]
rs10828911	0.95[AMR][1000 genomes]
rs10828965	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10828975	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10828983	0.86[ASN][1000 genomes]
rs10828991	0.88[ASN][1000 genomes]
rs10829009	0.88[ASN][1000 genomes]
rs10829022	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10829037	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10829039	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10829040	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10829058	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10829060	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10829070	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10829148	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10829151	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10829213	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11014892	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11015048	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11015077	0.86[ASN][1000 genomes]
rs11015196	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11015255	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11015312	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11015421	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11525266	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11540309	0.80[ASN][1000 genomes]
rs11812341	0.82[ASN][1000 genomes]
rs12219183	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12359758	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12569474	0.92[AMR][1000 genomes]
rs12762481	0.81[ASN][1000 genomes]
rs12780652	0.84[ASN][1000 genomes]
rs12785031	0.80[ASN][1000 genomes]
rs2272274	0.87[AMR][1000 genomes]
rs3740102	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740104	0.81[ASN][1000 genomes]
rs3817494	0.83[AMR][1000 genomes]
rs4747350	0.83[AMR][1000 genomes]
rs4748488	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4748492	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4748497	0.84[ASN][1000 genomes]
rs4748509	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5022622	0.88[ASN][1000 genomes]
rs56410858	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57066269	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57579336	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62634837	0.86[AMR][1000 genomes]
rs62634838	0.86[AMR][1000 genomes]
rs62636218	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6482533	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6482597	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7077722	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7079325	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7081461	0.86[ASN][1000 genomes]
rs7081690	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7081977	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7087030	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7099260	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7100880	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72787951	0.83[AMR][1000 genomes]
rs72787963	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7477076	0.88[ASN][1000 genomes]
rs7894016	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7895784	0.86[ASN][1000 genomes]
rs7898781	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7901598	0.95[AMR][1000 genomes]
rs7904263	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7909570	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7909845	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7910902	0.85[ASN][1000 genomes]
rs7917584	0.86[AMR][1000 genomes]
rs7922550	0.82[AMR][1000 genomes]
rs7922829	0.82[AMR][1000 genomes]
rs7923480	0.84[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
rs7899017	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs7899017	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs7899017	ARL5B	cis	Whole Blood	GTEx
rs7899017	RP11-499P20.2	cis	Whole Blood	GTEx
rs7899017	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7899017	RP11-499P20.2	cis	lung	GTEx
rs7899017	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs7899017	ARL5B	cis	multi-tissue	Pritchard
rs7899017	RP11-499P20.2	cis	Thyroid	GTEx
rs7899017	NSUN6	cis	lung	GTEx
rs7899017	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs7899017	RP11-499P20.2	cis	Nerve Tibial	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18941000-18945800	Weak transcription	Left Ventricle	heart
2	chr10:18941000-18947200	Weak transcription	Pancreas	Pancrea
3	chr10:18941000-18947200	Weak transcription	Thymus	Thymus
4	chr10:18941000-18947400	Weak transcription	Gastric	stomach
5	chr10:18941200-18945000	Weak transcription	Fetal Lung	lung
6	chr10:18941200-18946600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr10:18941200-18946600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:18941200-18946800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr10:18941200-18946800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr10:18941200-18946800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr10:18941200-18946800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr10:18941200-18946800	Weak transcription	NH-A	brain
13	chr10:18941200-18946800	Weak transcription	NHLF	lung
14	chr10:18941200-18947000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:18941200-18947000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr10:18941200-18947000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr10:18941200-18947000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:18941200-18947000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr10:18941200-18947000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr10:18941200-18947000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr10:18941200-18947000	Weak transcription	Brain Anterior Caudate	brain
22	chr10:18941200-18947000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:18941200-18947000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr10:18941200-18947000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr10:18941200-18947000	Weak transcription	Brain Substantia Nigra	brain
26	chr10:18941200-18947000	Weak transcription	Fetal Brain Male	brain
27	chr10:18941200-18947000	Weak transcription	Fetal Stomach	stomach
28	chr10:18941200-18947000	Weak transcription	Psoas Muscle	Psoas
29	chr10:18941200-18947000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr10:18941200-18947000	Weak transcription	HMEC	breast
31	chr10:18941200-18947000	Weak transcription	NHEK	skin
32	chr10:18941200-18947200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr10:18941200-18947200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr10:18941200-18947200	Weak transcription	Fetal Thymus	thymus
35	chr10:18941200-18947200	Weak transcription	HUVEC	blood vessel
36	chr10:18941400-18946000	Weak transcription	HepG2	liver
37	chr10:18941400-18946800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr10:18941400-18946800	Weak transcription	Adipose Nuclei	Adipose
39	chr10:18941400-18946800	Weak transcription	Fetal Heart	heart
40	chr10:18941400-18946800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr10:18941400-18947000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr10:18941400-18947000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr10:18941400-18947000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr10:18941400-18947000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr10:18941400-18947000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr10:18941400-18947000	Weak transcription	Brain Angular Gyrus	brain
47	chr10:18941400-18947000	Weak transcription	Colon Smooth Muscle	Colon
48	chr10:18941400-18947000	Weak transcription	A549	lung
49	chr10:18941400-18947200	Weak transcription	Primary B cells from cord blood	blood
50	chr10:18941400-18947200	Weak transcription	Brain Hippocampus Middle	brain

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