Variant report

Variant	rs10875762
Chromosome Location	chr12:48580759-48580760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48578276..48580987-chr12:48583534..48585807,2	K562	blood:
2	chr12:48575723..48577470-chr12:48580708..48582766,2	K562	blood:
3	chr12:48579750..48581259-chr12:48592126..48593668,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177875	Chromatin interaction
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1021313	0.86[ASN][1000 genomes]
rs10219623	0.83[ASN][1000 genomes]
rs10437919	0.86[ASN][1000 genomes]
rs10437920	0.86[ASN][1000 genomes]
rs10467101	0.88[ASN][1000 genomes]
rs10783234	0.91[ASN][1000 genomes]
rs10875745	0.81[ASN][1000 genomes]
rs10875747	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875748	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875750	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875756	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875764	0.92[ASN][1000 genomes]
rs10875767	0.90[ASN][1000 genomes]
rs10875768	0.88[ASN][1000 genomes]
rs10875769	0.83[ASN][1000 genomes]
rs10875770	0.90[ASN][1000 genomes]
rs10875772	0.88[ASN][1000 genomes]
rs10875777	0.86[ASN][1000 genomes]
rs10875778	0.86[ASN][1000 genomes]
rs10875779	0.86[ASN][1000 genomes]
rs10875782	0.83[ASN][1000 genomes]
rs11168413	0.81[ASN][1000 genomes]
rs11168414	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168418	0.81[ASN][1000 genomes]
rs11168420	0.81[EUR][1000 genomes]
rs11168422	0.81[ASN][1000 genomes]
rs11168425	0.80[ASN][1000 genomes]
rs11168427	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168433	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168450	0.92[ASN][1000 genomes]
rs11168459	0.90[ASN][1000 genomes]
rs11168483	0.83[ASN][1000 genomes]
rs11168487	0.86[ASN][1000 genomes]
rs11168508	0.81[ASN][1000 genomes]
rs11168510	0.81[ASN][1000 genomes]
rs11558768	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12227601	0.81[ASN][1000 genomes]
rs12297470	0.83[ASN][1000 genomes]
rs12300647	0.83[ASN][1000 genomes]
rs12305511	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12305647	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12310813	0.83[ASN][1000 genomes]
rs12312134	0.91[ASN][1000 genomes]
rs12317751	0.86[ASN][1000 genomes]
rs12318705	0.83[ASN][1000 genomes]
rs17122666	0.82[EUR][1000 genomes]
rs17122812	0.90[ASN][1000 genomes]
rs1859445	0.81[ASN][1000 genomes]
rs2012773	0.92[ASN][1000 genomes]
rs2107638	0.83[ASN][1000 genomes]
rs2171642	0.83[ASN][1000 genomes]
rs2228500	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2269935	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2286021	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2409005	0.81[ASN][1000 genomes]
rs2898065	0.85[ASN][1000 genomes]
rs2898066	0.81[ASN][1000 genomes]
rs4760622	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760625	0.81[ASN][1000 genomes]
rs4760681	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760687	0.88[ASN][1000 genomes]
rs4760689	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760690	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760695	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760696	0.92[ASN][1000 genomes]
rs4760697	0.91[ASN][1000 genomes]
rs61940962	0.90[ASN][1000 genomes]
rs61941003	0.86[ASN][1000 genomes]
rs61941006	0.86[ASN][1000 genomes]
rs6580659	0.90[ASN][1000 genomes]
rs7135779	0.92[ASN][1000 genomes]
rs716553	0.86[ASN][1000 genomes]
rs725454	0.81[EUR][1000 genomes]
rs7297298	0.81[ASN][1000 genomes]
rs7302466	0.83[ASN][1000 genomes]
rs7303055	0.86[ASN][1000 genomes]
rs7485355	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7486008	0.86[ASN][1000 genomes]
rs7486424	0.88[ASN][1000 genomes]
rs7975956	0.83[ASN][1000 genomes]
rs8804	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9634261	0.81[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10875762	RP1-228P16.1	cis	Esophagus Mucosa	GTEx
rs10875762	RP1-228P16.1	cis	lung	GTEx
rs10875762	RP1-228P16.1	cis	Thyroid	GTEx
rs10875762	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs10875762	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10875762	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48580000-48591000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:48580200-48583200	Weak transcription	Brain Angular Gyrus	brain
3	chr12:48580400-48581800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:48580400-48582000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48580400-48582400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:48580400-48583000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:48580400-48583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:48580400-48583400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:48580400-48583800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:48580400-48585600	Weak transcription	Esophagus	oesophagus

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