Variant report

Variant	rs10828835
Chromosome Location	chr10:18812436-18812437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10741099	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10764542	0.85[CEU][hapmap];0.85[ASN][1000 genomes]
rs10764566	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]
rs10764584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10828859	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][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];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10828970	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10829038	1.00[ASN][1000 genomes]
rs10829133	1.00[ASN][1000 genomes]
rs10829139	1.00[ASN][1000 genomes]
rs10829140	1.00[ASN][1000 genomes]
rs11014830	1.00[ASN][1000 genomes]
rs11014852	1.00[ASN][1000 genomes]
rs11015263	1.00[ASN][1000 genomes]
rs11015307	1.00[JPT][hapmap]
rs11015411	1.00[ASN][1000 genomes]
rs11015416	1.00[JPT][hapmap]
rs12359508	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12570585	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12765362	1.00[ASN][1000 genomes]
rs12771084	0.90[ASN][1000 genomes]
rs12772534	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352655	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17622920	1.00[JPT][hapmap]
rs1971272	1.00[JPT][hapmap]
rs2691159	1.00[ASN][1000 genomes]
rs4328135	0.91[ASN][1000 genomes]
rs4456162	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4475829	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4475830	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4484992	0.87[EUR][1000 genomes]
rs4578284	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634984	0.86[EUR][1000 genomes]
rs4636555	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4747353	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4748474	0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
rs4748480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4748489	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748491	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4748495	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4748508	1.00[ASN][1000 genomes]
rs6482516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6482529	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482534	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6482545	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7068575	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7070695	1.00[ASN][1000 genomes]
rs7071192	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7075151	0.80[EUR][1000 genomes]
rs7075304	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7077692	0.91[ASN][1000 genomes]
rs7078884	0.90[ASN][1000 genomes]
rs7080903	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082094	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084525	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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7090293	0.90[ASN][1000 genomes]
rs7091578	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092437	0.92[CEU][hapmap]
rs7095070	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7098313	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7098721	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7099975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101269	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7895235	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7895709	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7895775	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs7902450	1.00[JPT][hapmap]
rs7905730	1.00[JPT][hapmap]
rs7917323	1.00[JPT][hapmap]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10828835	RP11-499P20.2	cis	lung	GTEx
rs10828835	RP11-499P20.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:60 , 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	chr10:18809400-18812800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:18809800-18817800	Weak transcription	Fetal Stomach	stomach
25	chr10:18809800-18817800	Weak transcription	Pancreas	Pancrea
26	chr10:18810000-18812800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr10:18810400-18815400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr10:18810400-18816400	Weak transcription	Liver	Liver
29	chr10:18810400-18818400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr10:18810400-18828000	Weak transcription	Brain Angular Gyrus	brain
31	chr10:18810600-18813000	Weak transcription	Fetal Heart	heart
32	chr10:18810600-18827000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr10:18810600-18828200	Weak transcription	Aorta	Aorta
34	chr10:18810800-18812600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:18810800-18825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:18810800-18828000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:18811000-18816400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr10:18811000-18816400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr10:18811000-18816600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr10:18811000-18816600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:18811000-18817800	Weak transcription	Ovary	ovary
42	chr10:18811000-18817800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr10:18811000-18818200	Weak transcription	Left Ventricle	heart
44	chr10:18811000-18825400	Weak transcription	Right Ventricle	heart
45	chr10:18811000-18826800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr10:18811200-18816400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:18811200-18818800	Weak transcription	Fetal Lung	lung
48	chr10:18811200-18819000	Weak transcription	Fetal Intestine Large	intestine
49	chr10:18811600-18812600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr10:18812000-18812600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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