Variant report

Variant	rs1573601
Chromosome Location	chr13:48876357-48876358
allele	A/C
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	POLR2A	chr13:48876214-48877034	HepG2	liver:	n/a	n/a
2	RCOR1	chr13:48876262-48876389	K562	blood:	n/a	n/a
3	POLR2A	chr13:48875820-48878109	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:48806118..48810225-chr13:48876144..48879386,12	MCF-7	breast:
2	chr13:48851960..48854495-chr13:48874913..48877525,3	K562	blood:
3	chr13:48807200..48809098-chr13:48874367..48876486,2	K562	blood:

Variant related genes	Relation type
RB1	TF binding region
ENSG00000136156	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10219833	0.89[EUR][1000 genomes]
rs12100135	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12583516	0.89[ASN][1000 genomes]
rs12871662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12871740	0.85[EUR][1000 genomes]
rs12875750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1886795	0.85[EUR][1000 genomes]
rs1894255	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs1925744	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1925745	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1951775	0.85[CEU][hapmap]
rs1981434	0.90[CEU][hapmap]
rs198561	0.84[EUR][1000 genomes]
rs198563	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198584	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs198590	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198604	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs198607	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap]
rs198612	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198619	0.90[CEU][hapmap]
rs198634	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2243461	0.84[EUR][1000 genomes]
rs2243626	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs2248488	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs2251813	0.84[EUR][1000 genomes]
rs2253520	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2254423	0.84[EUR][1000 genomes]
rs2406933	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2854345	0.95[ASN][1000 genomes]
rs2854355	0.88[EUR][1000 genomes]
rs34217484	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs375105	0.81[EUR][1000 genomes]
rs3803188	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3809328	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3818455	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4151450	0.90[CEU][hapmap]
rs4151520	0.88[ASN][1000 genomes]
rs4594153	0.86[EUR][1000 genomes]
rs4600372	0.83[EUR][1000 genomes]
rs520342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61973349	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7358982	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7984554	0.85[EUR][1000 genomes]
rs7984795	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs7999447	0.85[EUR][1000 genomes]
rs8001315	0.85[EUR][1000 genomes]
rs9316367	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9316381	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap]
rs943278	0.86[CEU][hapmap]
rs9526465	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs9526466	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526470	0.91[EUR][1000 genomes]
rs9534998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535000	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535002	0.84[EUR][1000 genomes]
rs9535003	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535007	0.86[EUR][1000 genomes]
rs9535009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535011	0.89[EUR][1000 genomes]
rs9535032	0.86[CEU][hapmap]
rs9562815	0.86[ASN][1000 genomes]
rs9568025	0.87[ASN][1000 genomes]
rs9568026	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568027	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568028	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568029	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs9568032	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568033	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568034	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568035	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs990814	0.86[CEU][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1573601	ITM2B	cis	lymphoblastoid	seeQTL
rs1573601	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs1573601	C13orf1	cis	cerebellum	SCAN
rs1573601	ATAD2	trans	parietal	SCAN
rs1573601	LPAR6	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48844400-48877200	Weak transcription	Aorta	Aorta
2	chr13:48863000-48876400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr13:48866200-48876800	Weak transcription	Pancreas	Pancrea
4	chr13:48866200-48877200	Weak transcription	Left Ventricle	heart
5	chr13:48866600-48876600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:48868000-48876800	Weak transcription	Stomach Mucosa	stomach
7	chr13:48870200-48877000	Weak transcription	HSMMtube	muscle
8	chr13:48871000-48877000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr13:48871200-48877000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr13:48871400-48877000	Weak transcription	Primary B cells from cord blood	blood
11	chr13:48871600-48876600	Weak transcription	Brain Substantia Nigra	brain
12	chr13:48871600-48876800	Weak transcription	HepG2	liver
13	chr13:48871800-48876400	Weak transcription	K562	blood
14	chr13:48871800-48876800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr13:48871800-48877200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr13:48872000-48876800	Weak transcription	Thymus	Thymus
17	chr13:48873200-48876600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:48873400-48876800	Weak transcription	Primary T cells from cord blood	blood
19	chr13:48873400-48876800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr13:48874000-48876600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr13:48874200-48876400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr13:48874200-48876400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:48874800-48876400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr13:48875000-48876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr13:48875400-48876800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr13:48876000-48877000	Enhancers	Fetal Thymus	thymus
27	chr13:48876200-48876400	Enhancers	Dnd41	blood
28	chr13:48876200-48876600	Weak transcription	Fetal Kidney	kidney
29	chr13:48876200-48876600	Weak transcription	Fetal Lung	lung
30	chr13:48876200-48876800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr13:48876200-48877000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:48876200-48877200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links