Variant report

Variant	rs4475829
Chromosome Location	chr10:18886556-18886557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10828835	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10828859	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10828970	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12359508	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12569760	0.81[AMR][1000 genomes]
rs12570585	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12765362	0.85[AMR][1000 genomes]
rs12772534	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12781038	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4456162	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4475830	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4484992	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4578284	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4634984	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4636555	0.93[EUR][1000 genomes]
rs4748480	0.88[EUR][1000 genomes]
rs4748489	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4748491	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4748493	0.82[AFR][1000 genomes]
rs4748494	0.80[AFR][1000 genomes]
rs4748495	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6482529	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6482534	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6482545	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7068575	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7071192	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7073651	0.87[EUR][1000 genomes]
rs7075151	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7075304	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7080903	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7081811	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7082094	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7088214	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7090926	0.81[AFR][1000 genomes]
rs7091578	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7098721	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7099975	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7101269	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7895709	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7895775	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
10	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
11	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
12	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4475829	RP11-499P20.2	cis	lung	GTEx
rs4475829	NSUN6	cis	Nerve Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18846200-18899200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr10:18848400-18915800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr10:18849800-18910800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:18862200-18894600	Weak transcription	HSMM	muscle
5	chr10:18863000-18894600	Weak transcription	A549	lung
6	chr10:18863000-18910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:18863800-18902200	Weak transcription	Brain Anterior Caudate	brain
8	chr10:18864800-18898000	Weak transcription	Fetal Kidney	kidney
9	chr10:18866600-18899400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:18867600-18894400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:18867600-18899600	Weak transcription	Placenta	Placenta
12	chr10:18867800-18900400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr10:18867800-18916400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr10:18868000-18896400	Weak transcription	NHEK	skin
15	chr10:18868000-18902200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr10:18868000-18916200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:18868200-18896600	Weak transcription	Small Intestine	intestine
18	chr10:18868200-18904800	Weak transcription	HSMMtube	muscle
19	chr10:18868800-18896600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr10:18869800-18910800	Weak transcription	Right Ventricle	heart
21	chr10:18870200-18892000	Weak transcription	HepG2	liver
22	chr10:18870200-18900600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:18870400-18894400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:18870600-18908400	Weak transcription	Brain Substantia Nigra	brain
25	chr10:18870600-18916000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr10:18871000-18896400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr10:18871400-18895000	Weak transcription	Fetal Brain Male	brain
28	chr10:18871600-18910000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr10:18872000-18887200	Weak transcription	Fetal Heart	heart
30	chr10:18872400-18895000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr10:18872400-18899600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:18872800-18916000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:18873000-18894600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr10:18873200-18908200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr10:18873600-18896800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr10:18873600-18916000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr10:18875000-18916000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr10:18875600-18894600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:18875600-18895800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr10:18875600-18900600	Weak transcription	Esophagus	oesophagus
41	chr10:18875600-18912600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr10:18877000-18887200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr10:18877200-18891600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr10:18877200-18895000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr10:18877200-18896600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr10:18877200-18899200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr10:18877200-18899400	Weak transcription	K562	blood
48	chr10:18877200-18899600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr10:18877200-18916200	Weak transcription	Thymus	Thymus
50	chr10:18877200-18916400	Weak transcription	Spleen	Spleen

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