Variant report

Variant	rs12359508
Chromosome Location	chr10:18863690-18863691
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10741099	1.00[ASN][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764566	1.00[ASN][1000 genomes]
rs10764584	1.00[ASN][1000 genomes]
rs10828835	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828859	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828879	1.00[ASN][1000 genomes]
rs10828901	1.00[ASN][1000 genomes]
rs10828906	1.00[ASN][1000 genomes]
rs10828970	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10829038	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10829041	0.80[AFR][1000 genomes]
rs10829133	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10829139	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10829140	1.00[ASN][1000 genomes]
rs11014830	1.00[ASN][1000 genomes]
rs11014852	1.00[ASN][1000 genomes]
rs11015243	0.81[AFR][1000 genomes]
rs11015263	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11015307	0.81[AFR][1000 genomes]
rs11015411	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12412484	0.80[AFR][1000 genomes]
rs12569760	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12570585	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12765362	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12771084	0.90[ASN][1000 genomes]
rs12772534	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352655	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1968961	0.82[AFR][1000 genomes]
rs2691159	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4328135	0.91[ASN][1000 genomes]
rs4456162	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4475829	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4475830	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4484992	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4578284	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634984	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4636555	0.91[EUR][1000 genomes]
rs4747353	1.00[ASN][1000 genomes]
rs4748474	0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
rs4748480	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4748489	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748491	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4748495	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748503	0.82[AFR][1000 genomes]
rs4748508	1.00[ASN][1000 genomes]
rs6482516	1.00[ASN][1000 genomes]
rs6482529	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482534	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6482545	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7068575	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7070695	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7071192	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071897	0.81[AFR][1000 genomes]
rs7073651	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7075151	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7075304	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7077692	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7078884	0.90[ASN][1000 genomes]
rs7080903	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081811	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082094	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084525	0.88[AFR][1000 genomes];0.80[AMR][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	0.91[ASN][1000 genomes]
rs7088214	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7090293	0.90[ASN][1000 genomes]
rs7091578	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095070	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7098313	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7098721	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7099975	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101269	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7895235	1.00[ASN][1000 genomes]
rs7895709	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7895775	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv34545	chr10:18821185-18908294	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv1793653	chr10:18827828-18888369	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1794817	chr10:18827828-18888369	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv1811259	chr10:18827828-18888369	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	esv1840241	chr10:18827828-18888369	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv1841068	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	esv1851495	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	esv1835982	chr10:18833550-18872699	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2757371	chr10:18835325-18906507	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv2759736	chr10:18835325-18906507	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv466760	chr10:18839350-18905935	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv550044	chr10:18839350-18905935	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv1845973	chr10:18841795-18872699	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	esv1793359	chr10:18841795-18872872	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	esv1801825	chr10:18853581-18872699	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12359508	RP11-499P20.2	cis	lung	GTEx
rs12359508	NSUN6	cis	Nerve Tibial	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18840800-18867200	Weak transcription	Fetal Thymus	thymus
2	chr10:18842000-18866800	Weak transcription	Left Ventricle	heart
3	chr10:18842000-18868400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:18842000-18869200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:18842000-18886400	Weak transcription	Colon Smooth Muscle	Colon
6	chr10:18844000-18871000	Weak transcription	Fetal Heart	heart
7	chr10:18846200-18899200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:18846400-18866600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:18846600-18866600	Weak transcription	Pancreas	Pancrea
10	chr10:18848400-18915800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr10:18848800-18866800	Weak transcription	Aorta	Aorta
12	chr10:18849000-18868600	Weak transcription	Gastric	stomach
13	chr10:18849400-18866200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:18849800-18910800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr10:18850000-18865600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:18852600-18864800	Weak transcription	Ovary	ovary
17	chr10:18853200-18866800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr10:18859600-18868600	Weak transcription	K562	blood
19	chr10:18861000-18883200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr10:18861400-18864000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr10:18861600-18866200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:18861600-18867000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr10:18861800-18869000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr10:18862000-18866200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr10:18862200-18865600	Weak transcription	Adipose Nuclei	Adipose
26	chr10:18862200-18866800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:18862200-18868800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr10:18862200-18894600	Weak transcription	HSMM	muscle
29	chr10:18862400-18864400	Weak transcription	Primary T cells from cord blood	blood
30	chr10:18862400-18864800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr10:18862400-18865400	Weak transcription	Fetal Stomach	stomach
32	chr10:18862400-18865600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:18862400-18866000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr10:18862400-18866600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:18862400-18866600	Weak transcription	Fetal Intestine Large	intestine
36	chr10:18862400-18866800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr10:18862400-18866800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr10:18862400-18867000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr10:18862400-18878400	Strong transcription	Liver	Liver
40	chr10:18862600-18866200	Weak transcription	Dnd41	blood
41	chr10:18862600-18866800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr10:18862600-18866800	Weak transcription	Fetal Muscle Leg	muscle
43	chr10:18862600-18869200	Weak transcription	Fetal Brain Male	brain
44	chr10:18862600-18876600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:18862800-18864000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr10:18862800-18866200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr10:18862800-18866200	Weak transcription	Fetal Lung	lung
48	chr10:18863000-18864800	Weak transcription	Right Ventricle	heart
49	chr10:18863000-18867000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr10:18863000-18894600	Weak transcription	A549	lung

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