Variant report

Variant	rs6783003
Chromosome Location	chr3:49524778-49524779
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DAG1-1	chr3:49524687-49524848	NONHSAT089700
2	lnc-DAG1-1	chr3:49524661-49524848	NONHSAT089698

Extended variants
information (count: 85 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10155014	0.86[EUR][1000 genomes]
rs10865956	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1106620	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11130190	0.84[EUR][1000 genomes]
rs11715060	0.83[EUR][1000 genomes]
rs11719762	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11720657	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs11923032	0.81[EUR][1000 genomes]
rs11928090	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12583	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13096474	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13322887	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1464569	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1982861	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2140270	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2177268	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2312462	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2329025	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3448	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3866330	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3870339	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3870341	0.91[EUR][1000 genomes]
rs3905330	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4052546	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4241407	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4855837	0.89[EUR][1000 genomes]
rs4855853	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4855858	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4855869	0.89[EUR][1000 genomes]
rs4855882	0.82[YRI][hapmap]
rs4855885	1.00[YRI][hapmap]
rs4955424	0.81[EUR][1000 genomes]
rs4955425	0.80[EUR][1000 genomes]
rs4955430	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs56049603	0.80[EUR][1000 genomes]
rs56127630	0.87[EUR][1000 genomes]
rs56324858	0.84[EUR][1000 genomes]
rs57273516	0.93[EUR][1000 genomes]
rs62259933	0.91[EUR][1000 genomes]
rs62259943	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62259944	0.83[EUR][1000 genomes]
rs62259947	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62261183	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62261249	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6446262	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6446275	0.91[EUR][1000 genomes]
rs6446285	1.00[YRI][hapmap]
rs6769744	0.84[EUR][1000 genomes]
rs6775069	0.82[EUR][1000 genomes]
rs6784203	0.81[EUR][1000 genomes]
rs6785045	0.87[EUR][1000 genomes]
rs6805609	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6809204	0.81[EUR][1000 genomes]
rs72934271	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73073004	0.80[EUR][1000 genomes]
rs73088137	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7355800	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7374731	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7613491	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7619789	0.93[EUR][1000 genomes]
rs7620024	0.89[EUR][1000 genomes]
rs7622786	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7625857	0.89[EUR][1000 genomes]
rs7638750	0.83[EUR][1000 genomes]
rs7644148	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7647973	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7648995	0.87[EUR][1000 genomes]
rs7651372	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8897	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs940045	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9654010	0.89[EUR][1000 genomes]
rs974495	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9757181	1.00[CEU][hapmap]
rs9809237	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9817807	0.86[EUR][1000 genomes]
rs9824435	1.00[YRI][hapmap]
rs9842132	0.86[EUR][1000 genomes]
rs9860055	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9860285	0.81[AMR][1000 genomes]
rs9861027	0.87[EUR][1000 genomes]
rs9862534	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9871024	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9881860	1.00[CEU][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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs6783003	AMT	cis	Esophagus Muscularis	GTEx
rs6783003	WDR6	cis	Muscle Skeletal	GTEx
rs6783003	AMT	cis	Thyroid	GTEx
rs6783003	AMT	cis	Muscle Skeletal	GTEx
rs6783003	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs6783003	WDR6	cis	Nerve Tibial	GTEx
rs6783003	AMT	cis	lung	GTEx
rs6783003	ARIH2	cis	Thyroid	GTEx
rs6783003	NICN1-AS1	cis	Thyroid	GTEx
rs6783003	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs6783003	AMT	cis	Adipose Subcutaneous	GTEx
rs6783003	AMT	cis	Whole Blood	GTEx
rs6783003	NICN1	cis	Thyroid	GTEx
rs6783003	RHOA	cis	Muscle Skeletal	GTEx
rs6783003	AMT	cis	Artery Tibial	GTEx
rs6783003	AMT	cis	Nerve Tibial	GTEx
rs6783003	AMT	cis	Esophagus Mucosa	GTEx
rs6783003	AMT	cis	Artery Aorta	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509600-49530800	Weak transcription	Brain Germinal Matrix	brain
2	chr3:49509600-49537800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:49509800-49531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:49509800-49537600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:49510000-49526800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:49510000-49535600	Weak transcription	NHLF	lung
8	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:49514400-49532400	Weak transcription	GM12878-XiMat	blood
10	chr3:49514600-49548000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:49514800-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:49515000-49532800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:49515000-49535400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:49515200-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:49515200-49532400	Weak transcription	Colonic Mucosa	Colon
16	chr3:49515400-49531000	Weak transcription	Gastric	stomach
17	chr3:49515400-49547800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:49515400-49547800	Weak transcription	Fetal Brain Female	brain
19	chr3:49515400-49548800	Weak transcription	Esophagus	oesophagus
20	chr3:49516600-49526600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:49516800-49525600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:49516800-49532400	Weak transcription	Small Intestine	intestine
23	chr3:49516800-49534800	Weak transcription	Liver	Liver
24	chr3:49516800-49537600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:49517000-49525400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:49517000-49547800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:49517200-49524800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:49517200-49547800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:49517400-49530600	Weak transcription	Thymus	Thymus
30	chr3:49519200-49526000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:49519400-49530600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:49519400-49530800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr3:49519400-49535200	Weak transcription	K562	blood
34	chr3:49519600-49525800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:49520000-49530200	Weak transcription	Fetal Thymus	thymus
36	chr3:49520400-49532800	Weak transcription	Primary B cells from cord blood	blood
37	chr3:49521600-49525600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:49522200-49530600	Weak transcription	Aorta	Aorta
39	chr3:49522200-49530800	Weak transcription	Right Ventricle	heart
40	chr3:49522200-49547800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:49522400-49537800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:49522400-49548000	Weak transcription	Spleen	Spleen
43	chr3:49522800-49527200	Weak transcription	Left Ventricle	heart
44	chr3:49522800-49530200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:49522800-49531600	Weak transcription	Lung	lung
46	chr3:49523000-49525400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr3:49523000-49529800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:49523200-49531000	Weak transcription	Brain Anterior Caudate	brain
49	chr3:49523400-49524800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:49523400-49531000	Weak transcription	Brain Cingulate Gyrus	brain

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