Variant report

Variant	rs7898513
Chromosome Location	chr10:18801014-18801015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10400076	0.87[ASN][1000 genomes]
rs10508562	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs10508563	0.82[CHD][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs1055116	0.84[JPT][hapmap]
rs10741091	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10741111	0.85[JPT][hapmap]
rs10741115	0.86[JPT][hapmap]
rs10764578	0.86[ASN][1000 genomes]
rs10764582	0.90[JPT][hapmap]
rs10764601	0.86[JPT][hapmap]
rs10764625	0.81[JPT][hapmap]
rs10828851	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10828870	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs10828871	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs10828896	0.86[JPT][hapmap]
rs10828975	0.86[JPT][hapmap]
rs10829022	0.86[JPT][hapmap]
rs10829037	0.83[CHB][hapmap]
rs10829058	0.85[JPT][hapmap]
rs10829070	0.86[JPT][hapmap]
rs11014634	0.89[ASN][1000 genomes]
rs11014981	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs11015312	0.86[JPT][hapmap]
rs11511084	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs11540309	0.83[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs11815228	0.94[CHB][hapmap]
rs12762481	0.81[JPT][hapmap]
rs12764398	0.84[ASN][1000 genomes]
rs12766105	0.83[CHB][hapmap]
rs12766314	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs12767923	0.81[JPT][hapmap]
rs12769425	0.81[JPT][hapmap]
rs12772522	0.80[JPT][hapmap]
rs12774593	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs12778035	0.81[JPT][hapmap]
rs12779641	0.82[TSI][hapmap]
rs12781208	0.81[JPT][hapmap]
rs12784387	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.99[EUR][1000 genomes]
rs12784986	0.81[JPT][hapmap]
rs12785031	0.83[CHB][hapmap]
rs2228645	0.82[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs2272274	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs3740102	0.81[JPT][hapmap]
rs3740104	0.81[JPT][hapmap]
rs3817494	0.86[JPT][hapmap]
rs4237349	0.81[JPT][hapmap]
rs4314963	0.84[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs4445544	0.94[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs4468242	0.81[JPT][hapmap]
rs4747349	0.87[ASN][1000 genomes]
rs4747350	0.87[ASN][1000 genomes]
rs4748481	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]
rs4748482	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4748488	0.86[JPT][hapmap]
rs4748496	0.81[JPT][hapmap]
rs4748499	0.81[JPT][hapmap]
rs6482515	0.85[JPT][hapmap]
rs6482533	0.85[JPT][hapmap]
rs6482597	0.86[JPT][hapmap]
rs7072624	0.81[JPT][hapmap]
rs7072963	0.81[JPT][hapmap]
rs7081461	0.81[JPT][hapmap]
rs7088091	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7096923	0.81[JPT][hapmap];0.81[TSI][hapmap]
rs7099260	0.86[JPT][hapmap]
rs7099423	0.81[JPT][hapmap]
rs7100880	0.86[JPT][hapmap]
rs7895784	0.86[JPT][hapmap]
rs7904949	0.80[JPT][hapmap]
rs7917584	0.83[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs7922550	0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7922829	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7923480	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7898513	RP11-499P20.2	cis	Thyroid	GTEx
rs7898513	ARL5B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18732400-18801600	Weak transcription	Pancreas	Pancrea
2	chr10:18776200-18809400	Weak transcription	Right Ventricle	heart
3	chr10:18776200-18812200	Weak transcription	Right Atrium	heart
4	chr10:18778600-18818200	Weak transcription	Fetal Intestine Small	intestine
5	chr10:18779600-18803200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr10:18781000-18803200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:18785400-18808400	Weak transcription	Colon Smooth Muscle	Colon
8	chr10:18786800-18802000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr10:18787400-18807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr10:18787400-18808200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr10:18787400-18810200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr10:18787600-18803200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr10:18788000-18801800	Weak transcription	Fetal Stomach	stomach
14	chr10:18788200-18808400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr10:18788200-18809600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr10:18789800-18807800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr10:18790600-18802000	Weak transcription	Left Ventricle	heart
18	chr10:18790800-18801600	Weak transcription	Liver	Liver
19	chr10:18791000-18807200	Weak transcription	Brain Anterior Caudate	brain
20	chr10:18792400-18825400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr10:18794000-18818400	Weak transcription	Fetal Brain Male	brain
22	chr10:18795000-18801400	Weak transcription	Fetal Lung	lung
23	chr10:18795000-18803200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:18795000-18807200	Weak transcription	Aorta	Aorta
25	chr10:18795600-18801600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr10:18798400-18801600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr10:18798800-18801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr10:18799800-18803400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr10:18799800-18825200	Weak transcription	Colonic Mucosa	Colon
30	chr10:18800000-18801600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:18800200-18801400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr10:18800200-18826800	Weak transcription	Brain Substantia Nigra	brain
33	chr10:18800400-18827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr10:18800600-18802200	Strong transcription	Fetal Intestine Large	intestine
35	chr10:18800600-18803600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:18800800-18801600	Strong transcription	Fetal Heart	heart
37	chr10:18800800-18804000	Weak transcription	Ovary	ovary
38	chr10:18800800-18818800	Weak transcription	Brain Germinal Matrix	brain
39	chr10:18800800-18819400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr10:18801000-18818800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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