Variant report

Variant	rs58645732
Chromosome Location	chr3:42699475-42699476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13064597	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067987	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085143	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086680	0.91[EUR][1000 genomes]
rs13100261	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030458	0.81[EUR][1000 genomes]
rs2290976	0.93[EUR][1000 genomes]
rs339708	0.91[EUR][1000 genomes]
rs34077739	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34196076	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34243788	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34721465	0.90[EUR][1000 genomes]
rs35216140	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384559	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35871059	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36043081	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733059	0.93[EUR][1000 genomes]
rs3733061	0.91[EUR][1000 genomes]
rs3900780	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994846	1.00[ASN][1000 genomes]
rs56047094	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58825152	1.00[ASN][1000 genomes]
rs60535002	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66933062	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67174294	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67583158	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771105	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67832425	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790204	0.83[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6797491	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797545	1.00[ASN][1000 genomes]
rs68004576	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71323162	1.00[ASN][1000 genomes]
rs72864022	1.00[ASN][1000 genomes]
rs73067957	1.00[ASN][1000 genomes]
rs73829255	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614219	1.00[ASN][1000 genomes]
rs7616701	1.00[ASN][1000 genomes]
rs7623867	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1818302	chr3:42688867-42709062	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv876731	chr3:42690285-42711655	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58645732	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42696800-42701200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:42697000-42699800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:42697000-42699800	Weak transcription	Aorta	Aorta
4	chr3:42697000-42700000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:42697000-42700600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:42697000-42702400	Genic enhancers	Fetal Muscle Trunk	muscle
7	chr3:42697200-42699600	Weak transcription	Liver	Liver
8	chr3:42697200-42699800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr3:42697200-42701400	Genic enhancers	Fetal Muscle Leg	muscle
10	chr3:42697200-42703000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:42697200-42704600	Weak transcription	Primary B cells from cord blood	blood
12	chr3:42697400-42699600	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:42697400-42699600	Weak transcription	Gastric	stomach
14	chr3:42697400-42699800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:42697400-42699800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:42697400-42699800	Weak transcription	Ovary	ovary
17	chr3:42697400-42700000	Enhancers	HepG2	liver
18	chr3:42697400-42700200	Enhancers	Brain Substantia Nigra	brain
19	chr3:42697400-42700400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:42697400-42700800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:42697400-42701200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:42697400-42702000	Weak transcription	Fetal Kidney	kidney
23	chr3:42697400-42703000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:42697400-42706800	Weak transcription	HMEC	breast
25	chr3:42697400-42708800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:42697400-42708800	Weak transcription	Fetal Lung	lung
27	chr3:42697600-42699800	Enhancers	Brain Angular Gyrus	brain
28	chr3:42697600-42699800	Enhancers	Brain Anterior Caudate	brain
29	chr3:42697600-42699800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:42697600-42700000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr3:42697600-42700000	Weak transcription	Right Atrium	heart
32	chr3:42697600-42703400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:42697600-42704600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:42697600-42704800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:42697600-42707000	Weak transcription	A549	lung
36	chr3:42697600-42708000	Weak transcription	Colonic Mucosa	Colon
37	chr3:42697600-42709800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:42697800-42699800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:42697800-42699800	Weak transcription	Adipose Nuclei	Adipose
40	chr3:42697800-42699800	Weak transcription	Brain Germinal Matrix	brain
41	chr3:42697800-42700000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:42697800-42701000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:42697800-42702200	Weak transcription	HSMMtube	muscle
44	chr3:42697800-42702600	Genic enhancers	Brain Hippocampus Middle	brain
45	chr3:42697800-42707200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:42697800-42707600	Strong transcription	Fetal Intestine Small	intestine
47	chr3:42697800-42707800	Weak transcription	Psoas Muscle	Psoas
48	chr3:42697800-42709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:42698000-42699600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:42698000-42700000	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links