Variant report

Variant	rs13064597
Chromosome Location	chr3:42703265-42703266
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42695218..42698513-chr3:42700428..42704457,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230084	Chromatin interaction

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

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

rs_ID	r²[population]
rs13067987	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085143	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086680	0.90[EUR][1000 genomes]
rs13100261	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030458	0.80[EUR][1000 genomes]
rs2290976	0.94[EUR][1000 genomes]
rs339708	0.90[EUR][1000 genomes]
rs34077739	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34196076	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34243788	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34721465	0.91[EUR][1000 genomes]
rs35216140	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384559	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35871059	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36043081	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733059	0.91[EUR][1000 genomes]
rs3733061	0.93[EUR][1000 genomes]
rs3900780	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994846	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56047094	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58645732	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58825152	1.00[ASN][1000 genomes]
rs60535002	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66933062	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67174294	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67583158	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771105	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67832425	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790204	0.81[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6797491	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797545	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004576	0.83[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	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614219	1.00[ASN][1000 genomes]
rs7616701	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623867	0.84[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
rs13064597	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42697200-42704600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:42697400-42706800	Weak transcription	HMEC	breast
3	chr3:42697400-42708800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:42697400-42708800	Weak transcription	Fetal Lung	lung
5	chr3:42697600-42703400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:42697600-42704600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:42697600-42704800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:42697600-42707000	Weak transcription	A549	lung
9	chr3:42697600-42708000	Weak transcription	Colonic Mucosa	Colon
10	chr3:42697600-42709800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:42697800-42707200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:42697800-42707600	Strong transcription	Fetal Intestine Small	intestine
13	chr3:42697800-42707800	Weak transcription	Psoas Muscle	Psoas
14	chr3:42697800-42709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:42698000-42706400	Strong transcription	Fetal Stomach	stomach
16	chr3:42698200-42706600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:42698200-42708000	Weak transcription	HSMM	muscle
18	chr3:42698200-42708400	Weak transcription	HUVEC	blood vessel
19	chr3:42698400-42703800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:42698400-42704000	Genic enhancers	Right Ventricle	heart
21	chr3:42698800-42703400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:42699400-42703400	Strong transcription	NHEK	skin
23	chr3:42699800-42703800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
24	chr3:42699800-42704800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:42699800-42705000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:42699800-42705600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:42699800-42706800	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr3:42700000-42707000	Weak transcription	HepG2	liver
29	chr3:42700200-42704600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:42700200-42705800	Strong transcription	Lung	lung
31	chr3:42700400-42703800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:42700400-42705000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:42700800-42705600	Weak transcription	Ovary	ovary
34	chr3:42700800-42707600	Weak transcription	Adipose Nuclei	Adipose
35	chr3:42701200-42705800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:42701400-42703800	Strong transcription	Placenta	Placenta
37	chr3:42701400-42704400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:42701400-42704600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:42701400-42706200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:42701400-42708800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:42701600-42704000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:42701600-42706600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:42701600-42706600	Strong transcription	NHLF	lung
44	chr3:42701600-42706800	Weak transcription	Pancreas	Pancrea
45	chr3:42701600-42709000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:42701600-42709000	Weak transcription	Aorta	Aorta
47	chr3:42701800-42703400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:42701800-42705000	Weak transcription	Spleen	Spleen
49	chr3:42701800-42705200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:42701800-42709200	Weak transcription	NHDF-Ad	bronchial

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