Variant report

Variant	rs10828859
Chromosome Location	chr10:18822342-18822343
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:18822301-18822726	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000225527	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10741099	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10741100	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764566	0.80[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10764584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10828835	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];0.92[LWK][hapmap];1.00[ASN][1000 genomes]
rs10828970	0.84[AMR][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	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12570585	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12765362	1.00[ASN][1000 genomes]
rs12771084	0.90[ASN][1000 genomes]
rs12772534	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	0.84[AMR][1000 genomes];0.83[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]
rs1880682	0.81[GIH][hapmap];0.84[TSI][hapmap]
rs1971272	1.00[JPT][hapmap]
rs2691159	1.00[ASN][1000 genomes]
rs4328135	0.91[ASN][1000 genomes]
rs4456162	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4475829	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4475830	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4484992	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4578284	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634984	0.83[EUR][1000 genomes]
rs4636555	0.81[CEU][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap]
rs4747353	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4748474	1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
rs4748480	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4748489	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748491	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4748495	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	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482534	0.84[CEU][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6482545	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7068575	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7070695	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7071192	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073651	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7075151	0.81[AMR][1000 genomes]
rs7075304	0.81[AMR][1000 genomes]
rs7077692	0.91[ASN][1000 genomes]
rs7078884	0.90[ASN][1000 genomes]
rs7080903	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081811	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082094	0.83[AMR][1000 genomes];0.83[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	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7090293	0.90[ASN][1000 genomes]
rs7091578	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092437	0.84[CEU][hapmap]
rs7095070	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7098313	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs7098721	0.84[AMR][1000 genomes]
rs7099975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101269	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7895235	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7895709	0.84[CEU][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7895775	0.84[EUR][1000 genomes]
rs7902450	1.00[JPT][hapmap]
rs7905730	1.00[JPT][hapmap]
rs7907153	0.82[TSI][hapmap]
rs7917323	1.00[JPT][hapmap]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10828859	PTF1A	trans	cerebellum	SCAN
rs10828859	RP11-499P20.2	cis	lung	GTEx
rs10828859	ARL5B	cis	multi-tissue	Pritchard
rs10828859	NSUN6	cis	cerebellum	SCAN
rs10828859	NSUN6	cis	Nerve Tibial	GTEx
rs10828859	ARL5B	cis	lymphoblastoid	seeQTL
rs10828859	OLAH	cis	parietal	SCAN
rs10828859	NSUN6	cis	parietal	SCAN
rs10828859	PTPLA	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18792400-18825400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr10:18799800-18825200	Weak transcription	Colonic Mucosa	Colon
3	chr10:18800200-18826800	Weak transcription	Brain Substantia Nigra	brain
4	chr10:18800400-18827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:18802000-18825000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:18802600-18828000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:18802600-18828200	Weak transcription	Lung	lung
8	chr10:18807200-18826800	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:18807400-18828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:18808000-18828000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:18808400-18827000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr10:18808800-18825400	Weak transcription	Fetal Brain Female	brain
13	chr10:18809000-18824000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:18809000-18827000	Weak transcription	Small Intestine	intestine
15	chr10:18810400-18828000	Weak transcription	Brain Angular Gyrus	brain
16	chr10:18810600-18827000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:18810600-18828200	Weak transcription	Aorta	Aorta
18	chr10:18810800-18825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:18810800-18828000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr10:18811000-18825400	Weak transcription	Right Ventricle	heart
21	chr10:18811000-18826800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:18812400-18825200	Weak transcription	Brain Anterior Caudate	brain
23	chr10:18812400-18827000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr10:18812600-18823000	Weak transcription	Colon Smooth Muscle	Colon
25	chr10:18812800-18827000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:18814000-18828000	Weak transcription	Esophagus	oesophagus
27	chr10:18814600-18825200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:18814600-18827000	Weak transcription	Thymus	Thymus
29	chr10:18814800-18825200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr10:18814800-18825400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr10:18814800-18827600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr10:18815000-18826800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr10:18815200-18825400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:18815200-18843600	Weak transcription	A549	lung
35	chr10:18815800-18828000	Weak transcription	K562	blood
36	chr10:18816400-18830400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr10:18816400-18841800	Strong transcription	Liver	Liver
38	chr10:18816800-18829600	Weak transcription	HSMMtube	muscle
39	chr10:18817400-18829000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr10:18818200-18824000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr10:18818200-18825800	Weak transcription	Psoas Muscle	Psoas
42	chr10:18818600-18824200	Weak transcription	Fetal Stomach	stomach
43	chr10:18818600-18825200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr10:18818600-18825200	Weak transcription	Pancreas	Pancrea
45	chr10:18818800-18828000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr10:18818800-18828400	Weak transcription	Fetal Thymus	thymus
47	chr10:18819000-18825400	Weak transcription	Brain Germinal Matrix	brain
48	chr10:18819200-18825600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr10:18819200-18826800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr10:18819200-18827000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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