Variant report

Variant	rs4748481
Chromosome Location	chr10:18816007-18816008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10400076	0.82[ASN][1000 genomes]
rs10508562	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs10508563	0.83[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1055116	0.81[JPT][hapmap]
rs10741091	0.89[JPT][hapmap]
rs10741111	0.82[JPT][hapmap]
rs10741115	0.83[JPT][hapmap]
rs10764578	0.84[ASN][1000 genomes]
rs10764582	0.88[JPT][hapmap]
rs10764601	0.83[JPT][hapmap]
rs10828851	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10828870	0.88[JPT][hapmap]
rs10828871	0.87[JPT][hapmap]
rs10828896	0.83[JPT][hapmap]
rs10828975	0.82[JPT][hapmap]
rs10829022	0.83[JPT][hapmap]
rs10829058	0.81[JPT][hapmap]
rs10829070	0.83[JPT][hapmap]
rs11014634	0.81[ASN][1000 genomes]
rs11014981	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11015312	0.83[JPT][hapmap]
rs11015435	0.81[CHB][hapmap]
rs11511084	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11540309	0.82[JPT][hapmap]
rs11815228	0.81[CHB][hapmap]
rs12762481	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs12764334	0.81[ASN][1000 genomes]
rs12764398	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12766314	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs12767546	0.81[ASN][1000 genomes]
rs12767923	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs12769425	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs12770851	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12772522	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs12774593	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12775446	0.81[ASN][1000 genomes]
rs12778035	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs12781208	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs12784387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12784986	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs2130531	0.81[CHB][hapmap]
rs2228645	0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2272274	0.88[JPT][hapmap]
rs3740104	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs3817494	0.82[JPT][hapmap]
rs4237349	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4310518	0.82[JPT][hapmap]
rs4314963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4445544	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4468242	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs4747350	0.84[ASN][1000 genomes]
rs4748482	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4748488	0.82[JPT][hapmap]
rs4748496	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4748499	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs6482515	0.88[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs6482533	0.82[JPT][hapmap]
rs6482597	0.82[JPT][hapmap]
rs7072624	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs7072963	0.89[JPT][hapmap]
rs7088091	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7096923	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs7099260	0.82[JPT][hapmap]
rs7099423	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs7100880	0.82[JPT][hapmap]
rs7895784	0.82[JPT][hapmap]
rs7898513	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7904016	0.88[JPT][hapmap]
rs7904949	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs7905365	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7917584	0.89[JPT][hapmap]
rs7922550	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7922829	0.94[JPT][hapmap];0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4748481	RP11-499P20.2	cis	Thyroid	GTEx
rs4748481	ARL5B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18778600-18818200	Weak transcription	Fetal Intestine Small	intestine
2	chr10:18792400-18825400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr10:18794000-18818400	Weak transcription	Fetal Brain Male	brain
4	chr10:18799800-18825200	Weak transcription	Colonic Mucosa	Colon
5	chr10:18800200-18826800	Weak transcription	Brain Substantia Nigra	brain
6	chr10:18800400-18827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:18800800-18818800	Weak transcription	Brain Germinal Matrix	brain
8	chr10:18800800-18819400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr10:18801000-18818800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr10:18802000-18825000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:18802600-18828000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr10:18802600-18828200	Weak transcription	Lung	lung
13	chr10:18807200-18826800	Weak transcription	Brain Hippocampus Middle	brain
14	chr10:18807400-18828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr10:18807600-18816400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr10:18807600-18818800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr10:18808000-18828000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr10:18808400-18827000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr10:18808800-18825400	Weak transcription	Fetal Brain Female	brain
20	chr10:18809000-18824000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:18809000-18827000	Weak transcription	Small Intestine	intestine
22	chr10:18809200-18819000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr10:18809800-18817800	Weak transcription	Fetal Stomach	stomach
24	chr10:18809800-18817800	Weak transcription	Pancreas	Pancrea
25	chr10:18810400-18816400	Weak transcription	Liver	Liver
26	chr10:18810400-18818400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr10:18810400-18828000	Weak transcription	Brain Angular Gyrus	brain
28	chr10:18810600-18827000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr10:18810600-18828200	Weak transcription	Aorta	Aorta
30	chr10:18810800-18825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:18810800-18828000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:18811000-18816400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr10:18811000-18816400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr10:18811000-18816600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:18811000-18816600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr10:18811000-18817800	Weak transcription	Ovary	ovary
37	chr10:18811000-18817800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr10:18811000-18818200	Weak transcription	Left Ventricle	heart
39	chr10:18811000-18825400	Weak transcription	Right Ventricle	heart
40	chr10:18811000-18826800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr10:18811200-18816400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr10:18811200-18818800	Weak transcription	Fetal Lung	lung
43	chr10:18811200-18819000	Weak transcription	Fetal Intestine Large	intestine
44	chr10:18812400-18816600	Weak transcription	Fetal Kidney	kidney
45	chr10:18812400-18825200	Weak transcription	Brain Anterior Caudate	brain
46	chr10:18812400-18827000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr10:18812600-18816400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:18812600-18823000	Weak transcription	Colon Smooth Muscle	Colon
49	chr10:18812800-18827000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:18813000-18816200	Enhancers	Fetal Heart	heart

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