Variant report

Variant	rs10764566
Chromosome Location	chr10:18810674-18810675
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	chr10:18809597..18811635-chr10:18812630..18814429,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10741099	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741100	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs10828835	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828859	0.80[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10828879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10828901	1.00[ASN][1000 genomes]
rs10828906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[ASN][1000 genomes]
rs10829038	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829133	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829139	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829140	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014830	1.00[ASN][1000 genomes]
rs11014852	1.00[ASN][1000 genomes]
rs11015243	0.80[EUR][1000 genomes]
rs11015263	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015306	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11015307	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11015411	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015416	1.00[JPT][hapmap]
rs12257556	0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs12359508	1.00[ASN][1000 genomes]
rs12569760	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12570585	0.95[ASN][1000 genomes]
rs12765362	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771084	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12772534	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	1.00[ASN][1000 genomes]
rs1352655	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17622920	1.00[JPT][hapmap]
rs1880682	0.92[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1968961	0.82[EUR][1000 genomes]
rs1971272	1.00[JPT][hapmap]
rs2691159	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4328135	0.91[ASN][1000 genomes]
rs4578284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4636555	0.84[TSI][hapmap]
rs4747353	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4748474	0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
rs4748480	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4748489	1.00[ASN][1000 genomes]
rs4748495	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4748503	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4748508	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6482529	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6482534	0.81[MEX][hapmap];0.87[TSI][hapmap]
rs7068575	0.95[ASN][1000 genomes]
rs7070695	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071192	1.00[ASN][1000 genomes]
rs7071897	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7073651	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7077692	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7078884	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7080903	1.00[ASN][1000 genomes]
rs7081811	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082094	1.00[ASN][1000 genomes]
rs7084525	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085332	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7085587	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7086034	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7086911	0.91[ASN][1000 genomes]
rs7088214	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.95[ASN][1000 genomes]
rs7090293	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7091578	1.00[ASN][1000 genomes]
rs7095070	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098313	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101352	0.83[EUR][1000 genomes]
rs7895235	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895709	0.81[MEX][hapmap];0.89[TSI][hapmap]
rs7902450	1.00[JPT][hapmap]
rs7905730	1.00[JPT][hapmap]
rs7907153	0.88[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7917323	1.00[JPT][hapmap]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	0.86[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10764566	NSUN6	cis	Nerve Tibial	GTEx
rs10764566	COMMD3	cis	cerebellum	SCAN
rs10764566	RP11-499P20.2	cis	lung	GTEx
rs10764566	CACNB2	cis	parietal	SCAN
rs10764566	RP11-499P20.2	cis	Adipose Subcutaneous	GTEx
rs10764566	NSUN6	cis	parietal	SCAN
rs10764566	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs10764566	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10764566	NSUN6	cis	cerebellum	SCAN
rs10764566	TRDMT1	cis	parietal	SCAN
rs10764566	NSUN6	cis	Skin Sun Exposed Lower leg	GTEx
rs10764566	NSUN6	cis	Adipose Subcutaneous	GTEx
rs10764566	ARL5B	cis	multi-tissue	Pritchard
rs10764566	CACNB2	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18776200-18812200	Weak transcription	Right Atrium	heart
2	chr10:18778600-18818200	Weak transcription	Fetal Intestine Small	intestine
3	chr10:18792400-18825400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr10:18794000-18818400	Weak transcription	Fetal Brain Male	brain
5	chr10:18799800-18825200	Weak transcription	Colonic Mucosa	Colon
6	chr10:18800200-18826800	Weak transcription	Brain Substantia Nigra	brain
7	chr10:18800400-18827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr10:18800800-18818800	Weak transcription	Brain Germinal Matrix	brain
9	chr10:18800800-18819400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr10:18801000-18818800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr10:18802000-18825000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr10:18802600-18828000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:18802600-18828200	Weak transcription	Lung	lung
14	chr10:18806800-18811200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:18807200-18810800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr10:18807200-18811000	Strong transcription	Ovary	ovary
17	chr10:18807200-18811000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr10:18807200-18826800	Weak transcription	Brain Hippocampus Middle	brain
19	chr10:18807400-18811000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:18807400-18811200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr10:18807400-18828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr10:18807600-18816400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:18807600-18818800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:18807800-18811000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr10:18807800-18811200	Strong transcription	Fetal Lung	lung
26	chr10:18808000-18810800	Strong transcription	Left Ventricle	heart
27	chr10:18808000-18828000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:18808400-18811000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:18808400-18811000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:18808400-18827000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr10:18808600-18810800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr10:18808600-18811400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr10:18808800-18811200	Strong transcription	Fetal Intestine Large	intestine
34	chr10:18808800-18825400	Weak transcription	Fetal Brain Female	brain
35	chr10:18809000-18824000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr10:18809000-18827000	Weak transcription	Small Intestine	intestine
37	chr10:18809200-18819000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr10:18809400-18812000	Weak transcription	Brain Anterior Caudate	brain
39	chr10:18809400-18812400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr10:18809400-18812800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr10:18809600-18811400	Strong transcription	Rectal Smooth Muscle	rectum
42	chr10:18809800-18817800	Weak transcription	Fetal Stomach	stomach
43	chr10:18809800-18817800	Weak transcription	Pancreas	Pancrea
44	chr10:18810000-18811000	Strong transcription	Brain Cingulate Gyrus	brain
45	chr10:18810000-18812800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr10:18810400-18811000	Genic enhancers	Right Ventricle	heart
47	chr10:18810400-18812200	Weak transcription	Colon Smooth Muscle	Colon
48	chr10:18810400-18815400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr10:18810400-18816400	Weak transcription	Liver	Liver
50	chr10:18810400-18818400	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links