Variant report

Variant	rs2248488
Chromosome Location	chr13:48829564-48829565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48823943..48826005-chr13:48829324..48832126,2	MCF-7	breast:
2	chr13:48807403..48809674-chr13:48828409..48830579,2	K562	blood:
3	chr13:48825760..48827717-chr13:48828186..48830367,2	MCF-7	breast:
4	chr13:48818705..48820484-chr13:48828248..48829795,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10219833	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12100135	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs12430215	0.82[CEU][hapmap]
rs12871662	0.85[EUR][1000 genomes]
rs12871740	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12875750	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs1573601	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs1886795	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1925744	0.87[EUR][1000 genomes]
rs1925745	0.87[EUR][1000 genomes]
rs1951775	0.85[CEU][hapmap]
rs1981434	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs1981435	0.84[EUR][1000 genomes]
rs198563	0.86[CEU][hapmap]
rs198604	0.81[CEU][hapmap]
rs198607	0.85[CEU][hapmap]
rs198612	0.82[CEU][hapmap]
rs198619	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2243461	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2243626	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251813	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253520	0.92[EUR][1000 genomes]
rs2254423	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2406933	0.92[EUR][1000 genomes]
rs34217484	0.93[EUR][1000 genomes]
rs3803188	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs3809328	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs3818455	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs399413	0.81[CEU][hapmap]
rs4151450	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs4594153	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4600372	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs520342	0.90[CEU][hapmap]
rs61973349	0.85[EUR][1000 genomes]
rs7322987	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7358982	0.93[EUR][1000 genomes]
rs7984554	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984795	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999447	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8001315	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316367	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs9316369	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs9526465	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526466	0.87[EUR][1000 genomes]
rs9526470	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526475	0.81[CEU][hapmap]
rs9534996	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534998	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs9535000	0.87[EUR][1000 genomes]
rs9535002	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535003	0.87[EUR][1000 genomes]
rs9535006	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs9535007	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535009	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs9535011	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535016	0.82[EUR][1000 genomes]
rs9535032	0.86[CEU][hapmap]
rs9568026	0.90[EUR][1000 genomes]
rs9568027	0.85[EUR][1000 genomes]
rs9568028	0.85[EUR][1000 genomes]
rs9568029	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9568031	0.80[EUR][1000 genomes]
rs9568035	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2248488	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48808400-48843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:48809600-48837400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:48810400-48830200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr13:48810800-48841000	Weak transcription	Hela-S3	cervix
5	chr13:48811200-48843800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr13:48811600-48829600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr13:48811600-48835600	Weak transcription	Fetal Brain Male	brain
8	chr13:48811600-48836800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr13:48813400-48829600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr13:48823200-48832800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:48823400-48833200	Weak transcription	Small Intestine	intestine
12	chr13:48825200-48834000	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr13:48825200-48837000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr13:48825400-48836800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr13:48825400-48841200	Strong transcription	Fetal Thymus	thymus
16	chr13:48825400-48844400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr13:48825800-48837400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr13:48826200-48840000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr13:48826400-48830200	Weak transcription	Brain Substantia Nigra	brain
20	chr13:48826400-48841200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:48826600-48833400	Weak transcription	Psoas Muscle	Psoas
22	chr13:48826600-48837000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr13:48826800-48832200	Weak transcription	NHLF	lung
24	chr13:48826800-48837400	Weak transcription	Right Atrium	heart
25	chr13:48826800-48842000	Weak transcription	K562	blood
26	chr13:48827200-48830200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr13:48827400-48833200	Strong transcription	Primary T cells from cord blood	blood
28	chr13:48827400-48836600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr13:48827400-48836800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr13:48827400-48840200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr13:48827600-48831200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr13:48827600-48831200	Strong transcription	Thymus	Thymus
33	chr13:48827600-48832200	Strong transcription	Fetal Kidney	kidney
34	chr13:48827600-48832600	Strong transcription	HUVEC	blood vessel
35	chr13:48827600-48834400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr13:48827600-48837000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr13:48827600-48838800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:48827600-48839000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr13:48827600-48839800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr13:48827600-48839800	Strong transcription	Dnd41	blood
41	chr13:48827600-48841000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr13:48827600-48843600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr13:48827800-48831200	Strong transcription	HSMMtube	muscle
44	chr13:48827800-48831200	Strong transcription	NH-A	brain
45	chr13:48827800-48832800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr13:48827800-48833800	Strong transcription	HMEC	breast
47	chr13:48827800-48835000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr13:48827800-48836600	Strong transcription	Primary B cells from cord blood	blood
49	chr13:48827800-48836600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr13:48827800-48837200	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links