Variant report

Variant	rs1009051
Chromosome Location	chr3:49521549-49521550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49521377..49523560-chr3:49535457..49537721,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 19 )

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

rs_ID	r²[population]
rs10155014	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10865956	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1106620	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11130190	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11130211	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11715060	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11719762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11720657	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs11721148	1.00[ASN][1000 genomes]
rs11923032	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11928090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12583	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13096474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13322887	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1352889	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1464569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1491983	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17080510	1.00[CHB][hapmap]
rs1982861	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2140270	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2177268	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2312462	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2329025	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3448	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34890793	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs3866330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3870339	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3870341	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3905330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4052546	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4241407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4855833	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4855837	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4855853	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4855858	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855869	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4955430	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs56127630	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56324858	0.83[EUR][1000 genomes]
rs57273516	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62259933	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62259943	0.85[EUR][1000 genomes]
rs62259944	0.82[EUR][1000 genomes]
rs62259947	0.86[EUR][1000 genomes]
rs62261183	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62261249	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6446262	0.82[EUR][1000 genomes]
rs6446275	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6769744	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6774202	1.00[CHB][hapmap]
rs6775069	0.83[EUR][1000 genomes]
rs6783003	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6785045	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6796147	0.80[AFR][1000 genomes]
rs6805609	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6809204	0.80[EUR][1000 genomes]
rs72934271	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73088137	0.88[EUR][1000 genomes]
rs7355800	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7374731	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7613491	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7619789	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7620024	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7622786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625857	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7638750	0.82[EUR][1000 genomes]
rs7644148	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7647973	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7648995	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7651372	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7653505	1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8897	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs940045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9654010	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs974495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9757181	1.00[CEU][hapmap];0.83[AFR][1000 genomes]
rs9809237	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9817807	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9842132	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9860055	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9861027	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9862534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9871024	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs1009051	AMT	cis	Esophagus Mucosa	GTEx
rs1009051	AMT	cis	Whole Blood	GTEx
rs1009051	WDR6	cis	Muscle Skeletal	GTEx
rs1009051	WDR6	cis	Nerve Tibial	GTEx
rs1009051	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs1009051	NICN1	cis	Thyroid	GTEx
rs1009051	AMT	cis	Artery Tibial	GTEx
rs1009051	AMT	cis	Adipose Subcutaneous	GTEx
rs1009051	NICN1-AS1	cis	Thyroid	GTEx
rs1009051	AMT	cis	Nerve Tibial	GTEx
rs1009051	WDR6	cis	Esophagus Muscularis	GTEx
rs1009051	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs1009051	AMT	cis	Thyroid	GTEx
rs1009051	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs1009051	AMT	cis	Artery Aorta	GTEx
rs1009051	WDR6	cis	lung	GTEx
rs1009051	AMT	cis	lung	GTEx
rs1009051	AMT	cis	Esophagus Muscularis	GTEx
rs1009051	AMT	cis	Muscle Skeletal	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509600-49522800	Weak transcription	Brain Angular Gyrus	brain
2	chr3:49509600-49530800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:49509600-49537800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:49509800-49522800	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:49509800-49522800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:49509800-49522800	Weak transcription	NHEK	skin
7	chr3:49509800-49523000	Weak transcription	Brain Substantia Nigra	brain
8	chr3:49509800-49531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:49509800-49537600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:49510000-49522800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:49510000-49523200	Weak transcription	Fetal Kidney	kidney
13	chr3:49510000-49526800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:49510000-49535600	Weak transcription	NHLF	lung
15	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49511400-49522800	Weak transcription	Stomach Mucosa	stomach
17	chr3:49514200-49522000	Weak transcription	NHDF-Ad	bronchial
18	chr3:49514400-49522000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:49514400-49522800	Weak transcription	Osteobl	bone
20	chr3:49514400-49532400	Weak transcription	GM12878-XiMat	blood
21	chr3:49514600-49521800	Weak transcription	HSMM	muscle
22	chr3:49514600-49548000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:49514800-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:49515000-49521800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:49515000-49532800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:49515000-49535400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:49515200-49521800	Weak transcription	HMEC	breast
28	chr3:49515200-49522800	Weak transcription	Adipose Nuclei	Adipose
29	chr3:49515200-49523000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:49515200-49524600	Weak transcription	Dnd41	blood
31	chr3:49515200-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:49515200-49532400	Weak transcription	Colonic Mucosa	Colon
33	chr3:49515400-49522000	Weak transcription	Brain Anterior Caudate	brain
34	chr3:49515400-49522000	Weak transcription	Hela-S3	cervix
35	chr3:49515400-49531000	Weak transcription	Gastric	stomach
36	chr3:49515400-49547800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:49515400-49547800	Weak transcription	Fetal Brain Female	brain
38	chr3:49515400-49548800	Weak transcription	Esophagus	oesophagus
39	chr3:49515600-49522000	Weak transcription	Spleen	Spleen
40	chr3:49515600-49523000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:49515600-49523000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:49516200-49521600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:49516600-49526600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:49516800-49521800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:49516800-49522600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:49516800-49522800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:49516800-49525600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:49516800-49532400	Weak transcription	Small Intestine	intestine
49	chr3:49516800-49534800	Weak transcription	Liver	Liver
50	chr3:49516800-49537600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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