Variant report

Variant	rs9332246
Chromosome Location	chr13:48806214-48806215
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	FOXA1	chr13:48806172-48806687	HepG2	liver:	n/a	n/a
2	RAD21	chr13:48805924-48806351	HepG2	liver:	n/a	n/a
3	CTCF	chr13:48806200-48806350	Caco-2	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:48806118..48810225-chr13:48876144..48879386,12	MCF-7	breast:
2	chr13:48612019..48613651-chr13:48806032..48808331,2	MCF-7	breast:
3	chr13:48805537..48807049-chr13:48830310..48832562,2	K562	blood:
4	chr13:48668651..48670754-chr13:48805441..48808765,3	MCF-7	breast:

Variant related genes	Relation type
ITM2B	TF binding region
ENSG00000139687	Chromatin interaction
ENSG00000136143	Chromatin interaction
ENSG00000231473	Chromatin interaction
ENSG00000136146	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1002865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11556899	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3092888	1.00[CEU][hapmap]
rs34692420	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4151434	1.00[CEU][hapmap]
rs4151442	1.00[CEU][hapmap]
rs4151448	1.00[CEU][hapmap]
rs4151452	1.00[CEU][hapmap]
rs4151456	1.00[CEU][hapmap]
rs4151474	1.00[CEU][hapmap]
rs4151479	0.92[YRI][hapmap]
rs4151522	0.92[YRI][hapmap]
rs4151524	0.92[YRI][hapmap]
rs4151525	1.00[CEU][hapmap]
rs56955865	0.87[ASN][1000 genomes]
rs60372626	0.87[ASN][1000 genomes]
rs73485077	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73485079	0.87[ASN][1000 genomes]
rs7993670	1.00[ASN][1000 genomes]
rs7996717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];1.00[ASN][1000 genomes]
rs7999809	0.87[ASN][1000 genomes]
rs8002352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8002765	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9332278	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs9332285	0.87[ASN][1000 genomes]
rs9332304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9595874	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9595875	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1043294	chr13:48762477-48810028	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48796000-48806800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:48804200-48806600	Enhancers	Fetal Intestine Large	intestine
3	chr13:48804400-48806400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr13:48804400-48806600	Enhancers	Fetal Intestine Small	intestine
5	chr13:48804600-48806800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:48804800-48806400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:48804800-48806400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr13:48804800-48806400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr13:48804800-48806400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:48804800-48806400	Enhancers	Stomach Mucosa	stomach
11	chr13:48804800-48806600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:48804800-48806800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr13:48805000-48806800	Flanking Active TSS	HepG2	liver
14	chr13:48805200-48806600	Enhancers	Fetal Lung	lung
15	chr13:48805400-48806400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr13:48805400-48806400	Enhancers	A549	lung
17	chr13:48805400-48806400	Weak transcription	NHEK	skin
18	chr13:48805400-48806600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr13:48805400-48806800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:48805800-48806400	Enhancers	K562	blood
21	chr13:48805800-48806600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:48805800-48806600	Enhancers	Brain Germinal Matrix	brain
23	chr13:48805800-48806600	Enhancers	Colon Smooth Muscle	Colon
24	chr13:48805800-48806600	Enhancers	Fetal Stomach	stomach
25	chr13:48805800-48806800	Weak transcription	Hela-S3	cervix
26	chr13:48806000-48806400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr13:48806000-48806400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:48806000-48806400	Enhancers	Brain Hippocampus Middle	brain
29	chr13:48806000-48806400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr13:48806000-48806400	Weak transcription	Osteobl	bone
31	chr13:48806000-48806600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr13:48806000-48806600	Enhancers	Brain Cingulate Gyrus	brain
33	chr13:48806000-48806600	Enhancers	Small Intestine	intestine
34	chr13:48806000-48806800	Enhancers	Placenta	Placenta
35	chr13:48806000-48806800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr13:48806000-48807000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr13:48806000-48808200	Active TSS	Primary hematopoietic stem cells	blood
38	chr13:48806200-48806400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
39	chr13:48806200-48806400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr13:48806200-48806400	Active TSS	Primary T cells from cord blood	blood
41	chr13:48806200-48806400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr13:48806200-48806400	Enhancers	Brain Anterior Caudate	brain
43	chr13:48806200-48806400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr13:48806200-48806400	Enhancers	Fetal Brain Female	brain
45	chr13:48806200-48806400	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr13:48806200-48806400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr13:48806200-48806600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
48	chr13:48806200-48806600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr13:48806200-48806600	Enhancers	Primary B cells from peripheral blood	blood
50	chr13:48806200-48806600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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