Variant report

Variant	rs12417989
Chromosome Location	chr11:65466002-65466003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65463670..65466251-chr11:65542574..65544907,2	K562	blood:
2	chr11:65464340..65466957-chr11:65635073..65636599,2	MCF-7	breast:
3	chr11:65460118..65463457-chr11:65463620..65467916,5	K562	blood:
4	chr11:65429955..65431628-chr11:65463619..65466319,2	MCF-7	breast:
5	chr11:65461801..65463555-chr11:65465034..65466802,3	K562	blood:
6	chr11:65465574..65468849-chr11:65659509..65661845,3	K562	blood:
7	chr11:65463676..65466407-chr11:65650763..65652793,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172638	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000239356	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11227247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12418567	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12418630	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12418683	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12419110	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12420405	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420618	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12421691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1962691	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1963977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075660	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2127510	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2236683	0.97[EUR][1000 genomes]
rs2306365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35927673	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36028748	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36091060	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36113281	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741378	0.81[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs4578394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4645916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4645917	0.90[EUR][1000 genomes]
rs4930158	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4930299	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55758897	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56115979	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56236098	0.81[EUR][1000 genomes]
rs7101916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107503	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7122081	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7122098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
2	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
3	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
6	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv897748	chr11:65392695-65466911	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv897755	chr11:65405300-65481166	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65459400-65466200	Enhancers	Stomach Mucosa	stomach
2	chr11:65462400-65468000	Enhancers	Brain Hippocampus Middle	brain
3	chr11:65462600-65467800	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr11:65463800-65474000	Weak transcription	Pancreas	Pancrea
5	chr11:65464000-65467400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:65464800-65474000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:65465200-65466800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:65465400-65467800	Enhancers	Brain Anterior Caudate	brain
9	chr11:65465600-65467000	Enhancers	Brain Cingulate Gyrus	brain
10	chr11:65465600-65467000	Enhancers	Brain Substantia Nigra	brain
11	chr11:65465800-65466200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:65465800-65466400	Enhancers	Brain Angular Gyrus	brain
13	chr11:65466000-65466200	Enhancers	HUVEC	blood vessel

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