Variant report

Variant	rs10764584
Chromosome Location	chr10:18835325-18835326
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	POLR2A	chr10:18834644-18835533	H1-neurons	neurons:	n/a	n/a
2	REST	chr10:18834391-18835539	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ENSG00000240291	TF binding region

Extended variants
information (count: 102 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10741099	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10741100	0.81[AFR][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs10764587	1.00[CEU][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10828835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10828859	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]
rs10828879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828901	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828906	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]
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	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014852	0.89[AMR][1000 genomes];0.95[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]
rs12247061	0.81[AFR][1000 genomes]
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];1.00[EUR][1000 genomes]
rs1971272	1.00[JPT][hapmap]
rs2691159	1.00[ASN][1000 genomes]
rs4328135	0.89[AMR][1000 genomes];0.94[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	0.84[CEU][hapmap]
rs4747353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748474	0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
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	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6482516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482529	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6482546	0.83[AMR][1000 genomes]
rs6482567	0.94[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	0.84[YRI][hapmap]
rs7077692	0.91[ASN][1000 genomes]
rs7077786	0.85[YRI][hapmap]
rs7078884	0.90[ASN][1000 genomes]
rs7079776	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7080903	1.00[ASN][1000 genomes]
rs7081271	1.00[CHD][hapmap]
rs7081811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7082094	1.00[ASN][1000 genomes]
rs7082235	0.95[CEU][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.93[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	0.85[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]
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	0.83[AMR][1000 genomes]
rs7895235	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7902450	1.00[JPT][hapmap]
rs7904365	0.81[AMR][1000 genomes]
rs7905730	1.00[JPT][hapmap]
rs7908550	0.86[AMR][1000 genomes]
rs7910506	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7911922	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7917323	1.00[JPT][hapmap]
rs7918933	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	1.00[ASN][1000 genomes]
rs7923072	1.00[CHD][hapmap];0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10764584	NSUN6	cis	parietal	SCAN
rs10764584	RPP38	cis	cerebellum	SCAN
rs10764584	NSUN6	cis	cerebellum	SCAN
rs10764584	NSUN6	cis	multi-tissue	Pritchard
rs10764584	TRDMT1	cis	parietal	SCAN
rs10764584	NSUN6	cis	Liver	GTEx
rs10764584	VIM	cis	cerebellum	SCAN
rs10764584	ARL5B	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 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	chr10:18820800-18841600	Weak transcription	Hela-S3	cervix
4	chr10:18822000-18840400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr10:18822000-18848000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr10:18822800-18841800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:18823600-18836600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr10:18824200-18846200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr10:18824200-18850600	Weak transcription	NHLF	lung
10	chr10:18825000-18835800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:18825600-18841800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr10:18827000-18835800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr10:18827200-18842000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr10:18827200-18845200	Weak transcription	NHEK	skin
15	chr10:18827400-18841600	Weak transcription	HMEC	breast
16	chr10:18827600-18839400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:18828600-18837800	Weak transcription	Psoas Muscle	Psoas
18	chr10:18828600-18838800	Weak transcription	Colonic Mucosa	Colon
19	chr10:18828600-18841600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr10:18828600-18841600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr10:18828600-18841800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:18828600-18841800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:18828600-18841800	Weak transcription	Pancreas	Pancrea
24	chr10:18828600-18843000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr10:18828600-18843400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr10:18828600-18844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr10:18828600-18845400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:18828800-18846000	Weak transcription	Spleen	Spleen
29	chr10:18829000-18840400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr10:18829000-18841800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr10:18829200-18851200	Weak transcription	Esophagus	oesophagus
32	chr10:18829800-18837400	Weak transcription	GM12878-XiMat	blood
33	chr10:18829800-18838000	Weak transcription	Right Ventricle	heart
34	chr10:18829800-18844000	Weak transcription	Brain Angular Gyrus	brain
35	chr10:18830000-18842000	Weak transcription	Fetal Brain Female	brain
36	chr10:18830000-18842400	Weak transcription	Brain Germinal Matrix	brain
37	chr10:18830200-18841400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr10:18830200-18841800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr10:18830200-18841800	Weak transcription	Aorta	Aorta
40	chr10:18830200-18851000	Weak transcription	Thymus	Thymus
41	chr10:18830400-18837000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr10:18830400-18837800	Weak transcription	Primary B cells from cord blood	blood
43	chr10:18830400-18838400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr10:18830400-18839200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr10:18830400-18840000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr10:18830400-18840200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr10:18830400-18840400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr10:18830400-18840400	Weak transcription	Brain Anterior Caudate	brain
49	chr10:18830400-18840400	Weak transcription	HSMMtube	muscle
50	chr10:18830400-18841600	Weak transcription	H9 Cell Line	embryonic stem cell

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