Variant report

Variant	rs10828906
Chromosome Location	chr10:18841795-18841796
allele	C/T
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	SP1	chr10:18841346-18842706	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr10:18841379-18842742	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
NSUN6	TF binding region

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10741086	0.82[CEU][hapmap]
rs10741099	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[ASN][1000 genomes]
rs10764584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764587	1.00[CEU][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10828834	0.82[CEU][hapmap]
rs10828835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10828859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[ASN][1000 genomes]
rs10828879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828901	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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]
rs10829156	1.00[CHD][hapmap]
rs11014830	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014852	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];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	1.00[ASN][1000 genomes]
rs12570585	0.95[ASN][1000 genomes]
rs12765362	1.00[ASN][1000 genomes]
rs12771084	0.90[ASN][1000 genomes]
rs12772534	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	1.00[ASN][1000 genomes]
rs1352655	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17622920	1.00[JPT][hapmap]
rs1917209	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1917823	0.82[CEU][hapmap]
rs1971272	1.00[JPT][hapmap]
rs2691159	1.00[ASN][1000 genomes]
rs4328135	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4338439	0.86[AMR][1000 genomes]
rs4578284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4747348	0.88[CEU][hapmap]
rs4747353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748474	0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
rs4748476	0.82[CEU][hapmap]
rs4748480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4748489	1.00[ASN][1000 genomes]
rs4748495	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4748508	1.00[ASN][1000 genomes]
rs62636215	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6482516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482529	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6482546	0.84[AMR][1000 genomes]
rs6482567	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs7068575	0.95[ASN][1000 genomes]
rs7070695	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7071192	1.00[ASN][1000 genomes]
rs7073651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7075678	0.90[YRI][hapmap];0.85[AMR][1000 genomes]
rs7077692	0.91[ASN][1000 genomes]
rs7077786	0.90[YRI][hapmap]
rs7078884	0.90[ASN][1000 genomes]
rs7079776	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7080903	1.00[ASN][1000 genomes]
rs7081271	1.00[CHD][hapmap]
rs7081811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7082094	1.00[ASN][1000 genomes]
rs7082235	0.94[CEU][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7090293	0.90[ASN][1000 genomes]
rs7091578	1.00[ASN][1000 genomes]
rs7093907	0.90[YRI][hapmap];0.85[AMR][1000 genomes]
rs7095070	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7095666	1.00[CHD][hapmap];0.80[MEX][hapmap]
rs7098313	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7099975	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7100884	0.84[AMR][1000 genomes]
rs7895235	1.00[ASN][1000 genomes]
rs7902450	1.00[JPT][hapmap]
rs7905730	1.00[JPT][hapmap]
rs7908550	0.84[AMR][1000 genomes]
rs7910506	0.94[CEU][hapmap];1.00[CHD][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7911922	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7917323	1.00[JPT][hapmap]
rs7918933	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	1.00[ASN][1000 genomes]
rs7923072	1.00[CHD][hapmap];0.80[MEX][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:44 , 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	esv1835982	chr10:18833550-18872699	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv511455	chr10:18837285-18854168	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases
13	nsv550043	chr10:18837285-18859153	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases
14	esv1814421	chr10:18839350-18862211	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases
15	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
16	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
17	esv18824	chr10:18841137-18862749	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
18	esv1815720	chr10:18841795-18853581	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
19	nsv550045	chr10:18841795-18854685	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
20	nsv550046	chr10:18841795-18855161	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
21	nsv550047	chr10:18841795-18855755	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
22	esv1847851	chr10:18841795-18857730	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
23	esv1850351	chr10:18841795-18857730	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
24	nsv550048	chr10:18841795-18857730	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
25	esv1808982	chr10:18841795-18858271	ZNF genes & repeats Weak transcription Enhancers Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
26	esv1817510	chr10:18841795-18858271	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
27	nsv550049	chr10:18841795-18858271	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
28	nsv550050	chr10:18841795-18858664	Strong transcription Weak transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
29	nsv550051	chr10:18841795-18859450	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
30	nsv550052	chr10:18841795-18860469	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
31	nsv550053	chr10:18841795-18861203	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
32	nsv550054	chr10:18841795-18862122	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
33	esv1802087	chr10:18841795-18862211	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
34	esv1805552	chr10:18841795-18862211	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
35	esv1807060	chr10:18841795-18862211	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
36	esv1812459	chr10:18841795-18862211	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
37	esv1834849	chr10:18841795-18862211	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
38	esv1836472	chr10:18841795-18862211	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
39	esv1842030	chr10:18841795-18862211	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
40	esv1850544	chr10:18841795-18862211	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
41	nsv550055	chr10:18841795-18862211	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
42	nsv550056	chr10:18841795-18862728	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
43	esv1845973	chr10:18841795-18872699	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
44	esv1793359	chr10:18841795-18872872	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10828906	ARL5B	cis	lymphoblastoid	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18815200-18843600	Weak transcription	A549	lung
2	chr10:18816400-18841800	Strong transcription	Liver	Liver
3	chr10:18822000-18848000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr10:18822800-18841800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:18824200-18846200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr10:18824200-18850600	Weak transcription	NHLF	lung
7	chr10:18825600-18841800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:18827200-18842000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr10:18827200-18845200	Weak transcription	NHEK	skin
10	chr10:18828600-18841800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr10:18828600-18841800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:18828600-18841800	Weak transcription	Pancreas	Pancrea
13	chr10:18828600-18843000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr10:18828600-18843400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr10:18828600-18844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr10:18828600-18845400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:18828800-18846000	Weak transcription	Spleen	Spleen
18	chr10:18829000-18841800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr10:18829200-18851200	Weak transcription	Esophagus	oesophagus
20	chr10:18829800-18844000	Weak transcription	Brain Angular Gyrus	brain
21	chr10:18830000-18842000	Weak transcription	Fetal Brain Female	brain
22	chr10:18830000-18842400	Weak transcription	Brain Germinal Matrix	brain
23	chr10:18830200-18841800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr10:18830200-18841800	Weak transcription	Aorta	Aorta
25	chr10:18830200-18851000	Weak transcription	Thymus	Thymus
26	chr10:18830400-18841800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr10:18830400-18841800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr10:18830400-18841800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr10:18830400-18841800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr10:18830400-18841800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr10:18830400-18841800	Weak transcription	Brain Substantia Nigra	brain
32	chr10:18830400-18841800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr10:18830400-18843000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr10:18830400-18856600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr10:18830600-18841800	Weak transcription	Brain Hippocampus Middle	brain
36	chr10:18830600-18841800	Weak transcription	Placenta	Placenta
37	chr10:18830600-18841800	Weak transcription	Gastric	stomach
38	chr10:18830600-18842200	Weak transcription	Small Intestine	intestine
39	chr10:18830600-18845000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:18830600-18846600	Weak transcription	NH-A	brain
41	chr10:18831000-18841800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr10:18831000-18846000	Weak transcription	Lung	lung
43	chr10:18831000-18850200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr10:18832200-18841800	Weak transcription	Fetal Kidney	kidney
45	chr10:18832400-18842400	Weak transcription	HepG2	liver
46	chr10:18832400-18843000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr10:18834000-18842000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr10:18834400-18847800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr10:18835000-18841800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr10:18835000-18842600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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