Variant report

Variant	rs11168441
Chromosome Location	chr12:48576054-48576055
allele	A/C/G
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	RFX5	chr12:48575846-48577828	SK-N-SH	brain:	n/a	chr12:48577379-48577396 chr12:48577380-48577395 chr12:48577344-48577359 chr12:48577343-48577360 chr12:48577344-48577359 chr12:48577341-48577356 chr12:48577380-48577395 chr12:48577344-48577359 chr12:48577380-48577395

Variant related genes	Relation type
C12orf68	TF binding region
ASB8	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10875743	1.00[CHB][hapmap]
rs10875749	1.00[CHB][hapmap]
rs10875753	1.00[CHB][hapmap];0.88[AMR][1000 genomes]
rs10875763	0.83[ASN][1000 genomes]
rs1107654	1.00[CHB][hapmap]
rs11168408	1.00[CHB][hapmap]
rs11168428	1.00[CHB][hapmap]
rs11168437	1.00[CHB][hapmap]
rs11168460	1.00[CHB][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs12228750	1.00[CHB][hapmap]
rs12368659	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12816820	1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1476607	1.00[CHB][hapmap]
rs2054905	1.00[CHB][hapmap]
rs2408955	1.00[CHB][hapmap]
rs3087716	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4760612	1.00[CHB][hapmap];0.80[YRI][hapmap]
rs4760679	1.00[CHB][hapmap]
rs6580654	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7139330	1.00[CHB][hapmap]
rs7297824	1.00[CHB][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs7301003	1.00[CHB][hapmap]
rs7307566	1.00[CHB][hapmap];0.89[YRI][hapmap]
rs7315820	1.00[CHB][hapmap];0.83[AFR][1000 genomes]
rs7486941	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7487682	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7975632	1.00[CHB][hapmap]
rs8716	1.00[CHB][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs973398	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11168441	RP1-228P16.1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48571200-48576200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48575800-48576600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:48576000-48576200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
4	chr12:48576000-48576200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:48576000-48576200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr12:48576000-48576200	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr12:48576000-48576200	Bivalent Enhancer	NHDF-Ad	bronchial
8	chr12:48576000-48576400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
9	chr12:48576000-48576600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48576000-48576600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:48576000-48576800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links