Variant report

Variant	rs4936565
Chromosome Location	chr11:120802006-120802007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:120669903..120670453-chr11:120801797..120802326,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10892647	0.95[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10892648	0.83[ASW][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs10892651	0.85[ASN][1000 genomes]
rs11218066	0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11218068	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs11218069	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs11218070	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11218071	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11218072	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11218074	0.87[ASN][1000 genomes]
rs11218075	0.87[ASN][1000 genomes]
rs12361041	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12419730	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs17124570	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17124575	0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2186621	0.85[ASN][1000 genomes]
rs35024210	0.85[ASN][1000 genomes]
rs3781816	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs3781817	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4935757	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4936566	0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7113018	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73007850	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73007893	0.83[ASN][1000 genomes]
rs73007896	0.83[ASN][1000 genomes]
rs7926317	0.91[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7939524	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053607	chr11:120540795-120802006	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1042469	chr11:120799275-120846585	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv541183	chr11:120799275-120846585	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4936565	FOXR1	cis	cerebellum	SCAN
rs4936565	IFT46	cis	cerebellum	SCAN
rs4936565	ABCG4	cis	parietal	SCAN
rs4936565	TBCEL	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120800200-120803200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:120800200-120805000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:120800200-120805000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:120800200-120808200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:120800400-120808400	Weak transcription	Brain Anterior Caudate	brain
6	chr11:120800600-120802600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:120800600-120802600	Weak transcription	Fetal Muscle Leg	muscle
8	chr11:120800600-120815200	Weak transcription	Brain Hippocampus Middle	brain
9	chr11:120800800-120805000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:120801000-120811400	Weak transcription	Fetal Lung	lung
11	chr11:120801800-120802200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr11:120801800-120802200	Enhancers	Ovary	ovary
13	chr11:120802000-120802200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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