Variant report

Variant	rs4748508
Chromosome Location	chr10:18958646-18958647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18956344..18959967-chr10:18962484..18965500,3	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10741099	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741100	0.80[EUR][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764566	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764584	1.00[ASN][1000 genomes]
rs10828835	1.00[ASN][1000 genomes]
rs10828859	1.00[ASN][1000 genomes]
rs10828879	1.00[ASN][1000 genomes]
rs10828901	1.00[ASN][1000 genomes]
rs10828906	1.00[ASN][1000 genomes]
rs10829038	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829041	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10829133	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829139	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829140	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014830	1.00[ASN][1000 genomes]
rs11014852	1.00[ASN][1000 genomes]
rs11015243	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11015263	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015306	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11015307	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11015411	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359508	1.00[ASN][1000 genomes]
rs12412484	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12569760	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12570585	0.95[ASN][1000 genomes]
rs12765362	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771084	0.90[ASN][1000 genomes]
rs12772534	1.00[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	1.00[ASN][1000 genomes]
rs1352655	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880682	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1968961	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2691159	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4328135	0.91[ASN][1000 genomes]
rs4456162	0.83[AMR][1000 genomes]
rs4578284	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4747353	1.00[ASN][1000 genomes]
rs4748474	0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
rs4748480	0.95[ASN][1000 genomes]
rs4748489	1.00[ASN][1000 genomes]
rs4748495	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4748503	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6482516	1.00[ASN][1000 genomes]
rs6482529	1.00[ASN][1000 genomes]
rs7068575	0.95[ASN][1000 genomes]
rs7070695	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071192	1.00[ASN][1000 genomes]
rs7071897	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7073651	0.95[ASN][1000 genomes]
rs7077692	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7078884	0.90[ASN][1000 genomes]
rs7080903	1.00[ASN][1000 genomes]
rs7081811	1.00[ASN][1000 genomes]
rs7082094	1.00[ASN][1000 genomes]
rs7084525	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085332	0.90[ASN][1000 genomes]
rs7085587	0.90[ASN][1000 genomes]
rs7086034	0.90[ASN][1000 genomes]
rs7086911	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7088214	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7090293	0.90[ASN][1000 genomes]
rs7091578	1.00[ASN][1000 genomes]
rs7095070	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098313	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099975	1.00[ASN][1000 genomes]
rs7101352	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7895235	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895709	0.82[AMR][1000 genomes]
rs7907153	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4748508	NSUN6	cis	Nerve Tibial	GTEx
rs4748508	RP11-499P20.2	cis	lung	GTEx
rs4748508	NSUN6	cis	Adipose Subcutaneous	GTEx
rs4748508	RP11-499P20.2	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 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	chr10:18950800-18962400	Weak transcription	Fetal Kidney	kidney
4	chr10:18951000-18961800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:18951000-18962400	Weak transcription	Fetal Lung	lung
6	chr10:18951000-18965800	Weak transcription	Colonic Mucosa	Colon
7	chr10:18951000-18966600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:18951000-18967400	Weak transcription	Esophagus	oesophagus
9	chr10:18951000-18971800	Weak transcription	Spleen	Spleen
10	chr10:18951000-18976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:18951200-18964400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr10:18951400-18962400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:18951400-18962800	Weak transcription	Fetal Brain Male	brain
14	chr10:18951400-18973800	Weak transcription	Aorta	Aorta
15	chr10:18954000-18959400	Weak transcription	Ovary	ovary
16	chr10:18954000-18960200	Weak transcription	Lung	lung
17	chr10:18954000-18966600	Strong transcription	Dnd41	blood
18	chr10:18954400-18962200	Weak transcription	Psoas Muscle	Psoas
19	chr10:18954400-18964400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr10:18954400-18967200	Weak transcription	Gastric	stomach
21	chr10:18954400-18969200	Weak transcription	Right Ventricle	heart
22	chr10:18954400-18973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr10:18954600-18959400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:18954800-18959800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:18954800-18962800	Weak transcription	K562	blood
26	chr10:18954800-18964800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr10:18955000-18972600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:18955200-18959400	Weak transcription	Brain Hippocampus Middle	brain
29	chr10:18955200-18967600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr10:18955400-18959400	Weak transcription	Fetal Brain Female	brain
31	chr10:18955400-18969200	Weak transcription	Brain Angular Gyrus	brain
32	chr10:18955600-18966600	Strong transcription	Primary B cells from cord blood	blood
33	chr10:18955600-18966600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr10:18955600-18968000	Weak transcription	Brain Substantia Nigra	brain
35	chr10:18955800-18960800	Strong transcription	Fetal Thymus	thymus
36	chr10:18955800-18961000	Strong transcription	Fetal Intestine Large	intestine
37	chr10:18955800-18966200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr10:18955800-18966600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr10:18956000-18966200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr10:18956000-18966200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr10:18956000-18966600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr10:18956000-18966800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr10:18956000-18970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr10:18956000-18972200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr10:18956200-18961800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr10:18956200-18973200	Weak transcription	Small Intestine	intestine
47	chr10:18956400-18959600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr10:18956400-18959600	Weak transcription	NHLF	lung
49	chr10:18956400-18960000	Weak transcription	NHDF-Ad	bronchial
50	chr10:18956400-18962800	Weak transcription	Hela-S3	cervix

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