Variant report

Variant	rs1062994
Chromosome Location	chr1:184675814-184675815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1061508	0.82[AMR][1000 genomes]
rs10911631	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911633	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911634	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911636	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911644	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911645	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11808675	0.85[EUR][1000 genomes]
rs12031028	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12124929	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126231	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12131285	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12133128	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12137438	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12184284	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12567225	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567226	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064605	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2333715	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2877994	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233120	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4651230	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662416	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs67359172	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs861574	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs861575	0.81[EUR][1000 genomes]
rs861576	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs861577	0.81[EUR][1000 genomes]
rs861583	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425338	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9425340	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425343	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425632	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9425634	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9425635	0.81[AMR][1000 genomes]
rs971081	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1010371	chr1:184663898-184709570	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1001244	chr1:184667198-184715195	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1849889	chr1:184667371-184718601	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1062994	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs1062994	EDEM3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184653200-184705000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:184654000-184710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:184654200-184701200	Weak transcription	Stomach Mucosa	stomach
4	chr1:184654200-184710000	Weak transcription	Esophagus	oesophagus
5	chr1:184656600-184684000	Weak transcription	Fetal Heart	heart
6	chr1:184658400-184706800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:184659200-184707000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:184659400-184676800	Weak transcription	Fetal Brain Male	brain
9	chr1:184660000-184704200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:184660800-184680400	Weak transcription	Right Ventricle	heart
11	chr1:184661000-184678600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:184661000-184705600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr1:184661200-184690400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:184661200-184707800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:184661400-184678600	Strong transcription	Liver	Liver
16	chr1:184661400-184690400	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:184661600-184693200	Strong transcription	Dnd41	blood
18	chr1:184662000-184698000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:184662200-184706600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:184662600-184699400	Weak transcription	Psoas Muscle	Psoas
21	chr1:184663200-184676600	Weak transcription	NHEK	skin
22	chr1:184663600-184679400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:184665200-184683800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:184665200-184706800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:184665600-184687600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:184665600-184700400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:184666000-184678400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:184666000-184691400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:184666200-184704600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:184667000-184681000	Strong transcription	Primary hematopoietic stem cells	blood
31	chr1:184668400-184686000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:184668400-184690400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:184668400-184690600	Strong transcription	Fetal Thymus	thymus
34	chr1:184668400-184707000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr1:184668600-184693000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:184669200-184688800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:184669200-184707000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:184669400-184687400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:184669400-184692600	Strong transcription	Osteobl	bone
40	chr1:184669400-184707000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:184669600-184690400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:184669800-184692600	Strong transcription	Placenta	Placenta
43	chr1:184670600-184681600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:184670800-184690200	Strong transcription	Fetal Intestine Large	intestine
45	chr1:184670800-184690400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:184671000-184680600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:184671000-184686200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:184671200-184678400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:184671200-184686200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:184671200-184687000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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