Variant report

Variant	rs1473295
Chromosome Location	chr2:182521578-182521579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10930974	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12991856	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13019917	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13029498	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13032132	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1866888	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3863938	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3863939	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3910661	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3910662	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3910664	0.93[ASW][hapmap];1.00[YRI][hapmap]
rs3910665	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3916026	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4018755	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4018756	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4666792	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6709122	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7570291	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7582095	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7583601	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7602634	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1014910	chr2:182375267-182544114	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv536065	chr2:182375267-182544114	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv834477	chr2:182438121-182593527	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1473295	TTC30A	cis	cerebellum	SCAN
rs1473295	DUSP19	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182520000-182521600	Active TSS	Fetal Intestine Large	intestine
2	chr2:182520000-182522000	Active TSS	Right Atrium	heart
3	chr2:182520000-182522200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr2:182520200-182521800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:182520200-182521800	Active TSS	Fetal Intestine Small	intestine
6	chr2:182520200-182521800	Active TSS	NHLF	lung
7	chr2:182520400-182521800	Active TSS	Aorta	Aorta
8	chr2:182520400-182521800	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr2:182520400-182522000	Active TSS	Duodenum Mucosa	Duodenum
10	chr2:182520400-182522200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:182520600-182521800	Active TSS	Brain Anterior Caudate	brain
12	chr2:182520600-182522200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:182520800-182522000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr2:182520800-182522000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
15	chr2:182520800-182522000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr2:182520800-182522200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:182520800-182522200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr2:182520800-182522200	Bivalent/Poised TSS	A549	lung
19	chr2:182521000-182521800	Bivalent/Poised TSS	Fetal Brain Female	brain
20	chr2:182521000-182522000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr2:182521000-182522000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr2:182521000-182522000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:182521000-182522000	Active TSS	Fetal Kidney	kidney
24	chr2:182521000-182522000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
25	chr2:182521000-182522000	Bivalent/Poised TSS	NHDF-Ad	bronchial
26	chr2:182521000-182522000	Bivalent/Poised TSS	Osteobl	bone
27	chr2:182521000-182522200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:182521000-182522200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:182521000-182522200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:182521000-182522200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:182521000-182522200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:182521000-182522200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:182521000-182522200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
34	chr2:182521000-182522200	Active TSS	Rectal Smooth Muscle	rectum
35	chr2:182521000-182522400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:182521000-182522400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
37	chr2:182521200-182521600	Bivalent Enhancer	Primary B cells from cord blood	blood
38	chr2:182521200-182521600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr2:182521200-182521600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:182521200-182521600	Active TSS	Colon Smooth Muscle	Colon
41	chr2:182521200-182521600	Flanking Bivalent TSS/Enh	Placenta	Placenta
42	chr2:182521200-182521600	Active TSS	Lung	lung
43	chr2:182521200-182521600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
44	chr2:182521200-182521600	Flanking Active TSS	HMEC	breast
45	chr2:182521200-182521600	Active TSS	HSMMtube	muscle
46	chr2:182521200-182521800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:182521200-182521800	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr2:182521200-182521800	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:182521200-182521800	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr2:182521200-182521800	Bivalent Enhancer	Liver	Liver

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