Variant report

Variant	rs1407439
Chromosome Location	chr13:50283115-50283116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50278932..50281646-chr13:50283033..50285356,2	K562	blood:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs2273817	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35526541	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742096	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs56006419	0.82[ASN][1000 genomes]
rs61959916	0.82[ASN][1000 genomes]
rs61959917	0.82[ASN][1000 genomes]
rs61959931	0.82[ASN][1000 genomes]
rs61959938	0.83[ASN][1000 genomes]
rs6561556	0.88[ASN][1000 genomes]
rs7321073	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7321709	0.82[ASN][1000 genomes]
rs7332209	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs734223	0.82[ASN][1000 genomes]
rs748678	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7982919	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs7983049	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7996689	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap]
rs7999786	1.00[JPT][hapmap]
rs9526599	0.83[CEU][hapmap]
rs9535314	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535318	0.80[AMR][1000 genomes]
rs9535320	0.80[AMR][1000 genomes]
rs9535323	0.80[AMR][1000 genomes]
rs9535325	0.80[AMR][1000 genomes]
rs9535327	0.80[AMR][1000 genomes]
rs9535346	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9535351	1.00[CHB][hapmap]

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	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1407439	ITM2B	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266000-50284200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:50266200-50285600	Weak transcription	NHLF	lung
3	chr13:50266200-50286000	Weak transcription	Psoas Muscle	Psoas
4	chr13:50266200-50289400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr13:50266200-50289600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr13:50266200-50295200	Weak transcription	Spleen	Spleen
7	chr13:50266200-50296000	Weak transcription	K562	blood
8	chr13:50266200-50298600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:50266200-50298800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr13:50266200-50307800	Weak transcription	Gastric	stomach
11	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr13:50266400-50289400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr13:50266400-50293600	Weak transcription	Colonic Mucosa	Colon
14	chr13:50266400-50295800	Weak transcription	Small Intestine	intestine
15	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
16	chr13:50267200-50289400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr13:50270400-50286400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:50271400-50284800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr13:50271400-50286400	Strong transcription	Dnd41	blood
20	chr13:50271400-50286800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:50271600-50284400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:50272400-50295000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:50272400-50296000	Weak transcription	Fetal Heart	heart
24	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
25	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr13:50274000-50286600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr13:50274200-50286400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr13:50274200-50286400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr13:50275200-50284800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:50275400-50286400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr13:50275800-50289200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr13:50275800-50290000	Weak transcription	Brain Substantia Nigra	brain
33	chr13:50276000-50283200	Weak transcription	Ovary	ovary
34	chr13:50276000-50285000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr13:50276000-50286400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr13:50276000-50288400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr13:50276000-50289600	Weak transcription	Fetal Brain Male	brain
38	chr13:50276000-50289600	Weak transcription	Fetal Brain Female	brain
39	chr13:50276000-50291800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr13:50276000-50299800	Weak transcription	Right Ventricle	heart
41	chr13:50276000-50307600	Weak transcription	Pancreas	Pancrea
42	chr13:50276200-50285000	Weak transcription	HepG2	liver
43	chr13:50276200-50288600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr13:50277000-50283600	Weak transcription	GM12878-XiMat	blood
45	chr13:50277000-50318400	Weak transcription	Hela-S3	cervix
46	chr13:50277600-50286000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr13:50278000-50285200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr13:50278000-50286400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr13:50278200-50285200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr13:50278800-50284800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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