Variant report

Variant	rs62465512
Chromosome Location	chr7:65636933-65636934
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	chr7:65614360..65616994-chr7:65636358..65639293,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs12530506	0.87[EUR][1000 genomes]
rs12530746	0.89[EUR][1000 genomes]
rs12530898	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12531358	0.85[AMR][1000 genomes]
rs12531900	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12532327	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12532423	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12532675	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12533387	0.89[EUR][1000 genomes]
rs12534109	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12534249	0.89[EUR][1000 genomes]
rs12534477	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12534881	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535985	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12536816	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537039	0.89[EUR][1000 genomes]
rs12537407	0.85[AMR][1000 genomes]
rs12537698	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12537936	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12538147	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538379	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12538961	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12540307	0.80[EUR][1000 genomes]
rs12540888	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1363056	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2279904	1.00[AFR][1000 genomes]
rs2292936	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292937	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35832738	1.00[AFR][1000 genomes]
rs35910256	0.89[EUR][1000 genomes]
rs3735141	1.00[AFR][1000 genomes]
rs3735145	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3815684	0.89[EUR][1000 genomes]
rs4149467	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4717291	0.89[EUR][1000 genomes]
rs4718342	0.89[EUR][1000 genomes]
rs62465362	0.89[EUR][1000 genomes]
rs62465363	0.84[EUR][1000 genomes]
rs62465364	0.87[EUR][1000 genomes]
rs62465365	0.85[EUR][1000 genomes]
rs62465367	0.87[EUR][1000 genomes]
rs62465372	0.89[EUR][1000 genomes]
rs62465373	0.89[EUR][1000 genomes]
rs62465474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465476	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465483	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465484	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465519	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465521	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465522	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465525	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465526	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465527	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465542	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465545	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62465546	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465547	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465550	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465552	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465554	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467382	1.00[AFR][1000 genomes]
rs62467384	1.00[AFR][1000 genomes]
rs62467385	1.00[AFR][1000 genomes]
rs62467386	1.00[AFR][1000 genomes]
rs62467410	1.00[AFR][1000 genomes]
rs62467411	1.00[AFR][1000 genomes]
rs62467413	1.00[AFR][1000 genomes]
rs62467414	1.00[AFR][1000 genomes]
rs62467421	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62467436	0.85[AMR][1000 genomes]
rs62467437	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62467441	0.85[AMR][1000 genomes]
rs62467442	0.85[AMR][1000 genomes]
rs62467444	0.85[AMR][1000 genomes]
rs62467450	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62468669	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62468673	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62468674	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62468677	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62468679	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62468696	0.89[EUR][1000 genomes]
rs62468699	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62468700	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62468702	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62468705	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62468707	0.87[EUR][1000 genomes]
rs62468708	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62468709	0.81[EUR][1000 genomes]
rs62468711	0.89[EUR][1000 genomes]
rs62468712	0.84[EUR][1000 genomes]
rs62470926	1.00[AFR][1000 genomes]
rs62470931	1.00[AFR][1000 genomes]
rs62470934	1.00[AFR][1000 genomes]
rs62470940	1.00[AFR][1000 genomes]
rs62470945	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv971172	chr7:65616238-65653268	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62465512	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65626400-65637600	Weak transcription	Fetal Brain Female	brain
2	chr7:65636000-65638200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:65636000-65639200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:65636000-65639600	Weak transcription	Right Atrium	heart
5	chr7:65636000-65643200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr7:65636200-65637400	Weak transcription	Fetal Stomach	stomach
7	chr7:65636200-65638000	Weak transcription	Fetal Lung	lung
8	chr7:65636200-65638800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:65636200-65639800	Weak transcription	NHDF-Ad	bronchial
10	chr7:65636200-65641600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:65636200-65648200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:65636800-65637000	Enhancers	Fetal Brain Male	brain
13	chr7:65636800-65648000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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