Variant report

Variant	rs12273912
Chromosome Location	chr11:62698085-62698086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:62697029..62698908-chr11:62701103..62705116,3	MCF-7	breast:
2	chr11:62691791..62695911-chr11:62696538..62699345,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241082	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11231283	0.81[YRI][hapmap]
rs11822922	1.00[EUR][1000 genomes]
rs1787724	1.00[EUR][1000 genomes]
rs2510538	1.00[EUR][1000 genomes]
rs2584915	1.00[EUR][1000 genomes]
rs2584917	1.00[EUR][1000 genomes]
rs2730030	1.00[EUR][1000 genomes]
rs2956139	1.00[EUR][1000 genomes]
rs2958240	1.00[EUR][1000 genomes]
rs481272	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs482331	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs486451	1.00[EUR][1000 genomes]
rs489275	1.00[EUR][1000 genomes]
rs4963309	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs506132	1.00[EUR][1000 genomes]
rs507101	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs514401	1.00[EUR][1000 genomes]
rs518780	1.00[EUR][1000 genomes]
rs519473	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs523328	1.00[EUR][1000 genomes]
rs544573	1.00[EUR][1000 genomes]
rs560618	1.00[EUR][1000 genomes]
rs561385	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs56226867	1.00[EUR][1000 genomes]
rs56262657	1.00[EUR][1000 genomes]
rs564587	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs572513	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs573146	1.00[EUR][1000 genomes]
rs57338459	1.00[EUR][1000 genomes]
rs575134	1.00[EUR][1000 genomes]
rs577071	1.00[EUR][1000 genomes]
rs57858466	1.00[EUR][1000 genomes]
rs592337	1.00[EUR][1000 genomes]
rs595108	1.00[EUR][1000 genomes]
rs60568977	1.00[EUR][1000 genomes]
rs60668695	1.00[EUR][1000 genomes]
rs619109	1.00[EUR][1000 genomes]
rs646194	1.00[EUR][1000 genomes]
rs692773	1.00[EUR][1000 genomes]
rs694678	1.00[EUR][1000 genomes]
rs73487834	1.00[EUR][1000 genomes]
rs73487878	1.00[EUR][1000 genomes]
rs73487879	1.00[EUR][1000 genomes]
rs73487880	1.00[EUR][1000 genomes]
rs73490026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv1041770	chr11:62610353-62871767	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	263 gene(s)	inside rSNPs	diseases
4	esv34011	chr11:62652779-62993702	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12273912	GPR171	trans	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62695800-62699600	Enhancers	Brain Germinal Matrix	brain
2	chr11:62696000-62699000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:62696000-62701400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:62696600-62701400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:62696800-62700400	Enhancers	Fetal Muscle Trunk	muscle
6	chr11:62697000-62698200	Enhancers	Fetal Lung	lung
7	chr11:62697200-62698400	Enhancers	Fetal Heart	heart
8	chr11:62697200-62698800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:62697200-62699600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr11:62697400-62699400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:62697600-62698200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
12	chr11:62697600-62700400	Enhancers	Fetal Muscle Leg	muscle
13	chr11:62697800-62699200	Enhancers	Fetal Stomach	stomach
14	chr11:62697800-62699400	Enhancers	Fetal Intestine Large	intestine
15	chr11:62697800-62702000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr11:62698000-62698200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:62698000-62698400	Bivalent Enhancer	Fetal Intestine Small	intestine
18	chr11:62698000-62699000	Weak transcription	Brain Cingulate Gyrus	brain

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