Variant report

Variant	rs861576
Chromosome Location	chr1:184725397-184725398
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	MXI1	chr1:184722533-184725625	SK-N-SH	brain:	n/a	chr1:184724823-184724832
2	CUX1	chr1:184723849-184725665	K562	blood:	n/a	n/a
3	HCFC1	chr1:184722571-184725624	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184722993..184726139-chr1:185013897..185016469,4	K562	blood:

Variant related genes	Relation type
EDEM3	TF binding region
ENSG00000121481	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1062994	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911631	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911633	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911634	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911636	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911644	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911645	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11808675	0.86[EUR][1000 genomes]
rs12031028	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12124929	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126231	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12131285	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133128	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12137438	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12184284	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12567225	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12567226	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2064605	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2333715	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2877994	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4651230	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67359172	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs861574	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs861575	0.90[EUR][1000 genomes]
rs861577	0.90[EUR][1000 genomes]
rs861583	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425338	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425340	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9425343	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425632	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425634	0.87[ASN][1000 genomes]
rs971081	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][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	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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs861576	EDEM3	cis	Esophagus Muscularis	GTEx
rs861576	EDEM3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184722200-184725400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:184722600-184725400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:184723000-184725400	Active TSS	Brain Anterior Caudate	brain
4	chr1:184723000-184725400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:184723000-184725400	Active TSS	A549	lung
6	chr1:184724400-184725400	Flanking Active TSS	Osteobl	bone
7	chr1:184724600-184725400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr1:184724600-184725400	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr1:184724600-184725400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr1:184724600-184725400	Flanking Active TSS	Dnd41	blood
11	chr1:184724600-184725400	Flanking Active TSS	HMEC	breast
12	chr1:184724600-184725400	Flanking Active TSS	NH-A	brain
13	chr1:184724600-184725400	Flanking Active TSS	NHEK	skin
14	chr1:184724600-184728800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:184724800-184725400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:184724800-184725400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:184724800-184742600	Weak transcription	Gastric	stomach
18	chr1:184725000-184725400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:184725000-184725400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:184725000-184725400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:184725000-184725400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:184725000-184725400	Enhancers	Colon Smooth Muscle	Colon
23	chr1:184725000-184725600	Flanking Active TSS	K562	blood
24	chr1:184725000-184725800	Weak transcription	Pancreas	Pancrea
25	chr1:184725000-184728400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:184725200-184725400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr1:184725200-184725400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:184725200-184725400	Enhancers	Primary T cells from cord blood	blood
29	chr1:184725200-184725400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:184725200-184725400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:184725200-184725400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr1:184725200-184725400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:184725200-184725400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:184725200-184725400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:184725200-184725400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:184725200-184725400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr1:184725200-184725400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:184725200-184725400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:184725200-184725400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:184725200-184725400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:184725200-184725400	Enhancers	Adipose Nuclei	Adipose
42	chr1:184725200-184725400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr1:184725200-184725400	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr1:184725200-184725400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr1:184725200-184725400	Enhancers	Fetal Heart	heart
46	chr1:184725200-184725400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:184725200-184725400	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr1:184725200-184725400	Flanking Active TSS	Stomach Mucosa	stomach
49	chr1:184725200-184725400	Flanking Active TSS	HepG2	liver
50	chr1:184725200-184725400	Enhancers	HUVEC	blood vessel

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