Variant report

Variant	rs4475248
Chromosome Location	chr5:151912699-151912700
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:151911947..151912904-chr5:151940236..151940763,2	MCF-7	breast:
2	chr5:151908575..151910710-chr5:151911212..151913134,2	MCF-7	breast:
3	chr5:151912240..151912915-chr5:153135713..153136561,3	MCF-7	breast:
4	chr5:151912337..151912919-chr5:153344415..153345399,3	MCF-7	breast:
5	chr5:151912365..151912880-chr5:153784343..153784915,2	MCF-7	breast:
6	chr5:151912318..151913241-chr5:153344663..153345462,5	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10036750	0.84[AMR][1000 genomes]
rs10045463	0.83[AMR][1000 genomes]
rs10053277	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061873	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17452090	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17549307	0.83[AMR][1000 genomes]
rs17549488	0.85[CHB][hapmap];0.83[AMR][1000 genomes]
rs28450108	0.81[AFR][1000 genomes]
rs28663290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687145	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961740	0.85[ASN][1000 genomes]
rs2961747	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964224	0.82[EUR][1000 genomes]
rs2964225	0.81[EUR][1000 genomes]
rs4246030	0.85[AMR][1000 genomes]
rs4342320	0.85[AMR][1000 genomes]
rs4407620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569857	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958557	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958559	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55858427	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56012817	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868942	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6885840	0.81[AFR][1000 genomes]
rs72795344	0.85[AMR][1000 genomes]
rs72795349	0.85[AMR][1000 genomes]
rs72795350	0.85[AMR][1000 genomes]
rs72795351	0.82[AMR][1000 genomes]
rs72795352	0.85[AMR][1000 genomes]
rs72795354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795364	0.83[AMR][1000 genomes]
rs72795366	0.82[AMR][1000 genomes]
rs765676	0.88[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	nsv1023828	chr5:151522149-151956217	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1028516	chr5:151896509-151930647	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4475248	CDX1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151909200-151913200	Weak transcription	Fetal Brain Female	brain
2	chr5:151909600-151914000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:151909800-151913200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:151910400-151913600	Weak transcription	Fetal Lung	lung
5	chr5:151912400-151912800	Enhancers	Brain Cingulate Gyrus	brain
6	chr5:151912400-151912800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:151912400-151912800	Flanking Active TSS	Fetal Brain Male	brain
8	chr5:151912400-151913000	Enhancers	Brain Germinal Matrix	brain
9	chr5:151912400-151913000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr5:151912600-151912800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:151912600-151913000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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