Variant report

Variant	rs4233120
Chromosome Location	chr1:184633717-184633718
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184595979..184598591-chr1:184630812..184634151,3	MCF-7	breast:
2	chr1:184044621..184045156-chr1:184632510..184633780,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EDEM3-3	chr1:184632551-184633736	NONHSAT008391

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1062994	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10752940	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10911631	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10911633	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10911634	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10911636	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10911644	0.91[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs10911645	0.84[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12031028	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12124929	0.87[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12126231	0.82[EUR][1000 genomes]
rs12131285	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12133128	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12137438	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12184284	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12567225	0.91[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12567226	0.91[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2064605	0.92[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2333715	0.91[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2877994	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4651230	0.91[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs6662416	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67359172	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9425338	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9425340	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9425343	0.91[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9425632	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs971081	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription 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	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv947339	chr1:184618714-184641256	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4233120	EDEM3	cis	Esophagus Muscularis	GTEx
rs4233120	EDEM3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184632600-184634000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr1:184632600-184634200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:184632600-184634200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr1:184632800-184633800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:184632800-184633800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:184632800-184633800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:184632800-184633800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:184632800-184633800	Active TSS	Fetal Brain Female	brain
9	chr1:184632800-184633800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr1:184632800-184633800	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr1:184632800-184634000	Active TSS	Brain Substantia Nigra	brain
12	chr1:184632800-184634200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:184632800-184634200	Enhancers	Spleen	Spleen
14	chr1:184632800-184634600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:184632800-184634800	Enhancers	Fetal Heart	heart
16	chr1:184632800-184635000	Enhancers	Fetal Brain Male	brain
17	chr1:184633000-184633800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr1:184633000-184633800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:184633000-184633800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:184633000-184633800	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr1:184633000-184633800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr1:184633000-184633800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
23	chr1:184633000-184633800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
24	chr1:184633000-184633800	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr1:184633000-184633800	Flanking Active TSS	HMEC	breast
26	chr1:184633000-184634000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:184633000-184634000	Enhancers	Lung	lung
28	chr1:184633000-184634200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:184633200-184633800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr1:184633200-184633800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:184633200-184633800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:184633200-184633800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:184633200-184633800	Active TSS	Brain Anterior Caudate	brain
34	chr1:184633200-184633800	Flanking Active TSS	Colonic Mucosa	Colon
35	chr1:184633200-184633800	Active TSS	Psoas Muscle	Psoas
36	chr1:184633200-184634000	Active TSS	Brain Angular Gyrus	brain
37	chr1:184633200-184634800	Enhancers	Fetal Lung	lung
38	chr1:184633400-184633800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr1:184633400-184633800	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr1:184633400-184633800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:184633400-184633800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr1:184633400-184633800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:184633400-184633800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr1:184633400-184633800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr1:184633400-184633800	Flanking Active TSS	Esophagus	oesophagus
46	chr1:184633400-184633800	Flanking Active TSS	Right Ventricle	heart
47	chr1:184633400-184634000	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr1:184633600-184633800	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr1:184633600-184633800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:184633600-184633800	Enhancers	Primary monocytes fromperipheralblood	blood

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