Variant report

Variant	rs12538054
Chromosome Location	chr7:66638510-66638511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12530524	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12530887	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12532208	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12532995	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12535023	0.81[ASN][1000 genomes]
rs12536147	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12536460	1.00[AFR][1000 genomes]
rs12537633	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12538144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540025	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs62464960	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62464964	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs62464966	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62464967	0.94[ASN][1000 genomes]
rs62464968	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62464972	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62464974	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62464975	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62464976	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62464977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62465000	0.88[AMR][1000 genomes]
rs62466618	1.00[AFR][1000 genomes]
rs62466620	1.00[AFR][1000 genomes]
rs62466625	1.00[AFR][1000 genomes]
rs62468374	0.80[ASN][1000 genomes]
rs62468378	0.81[ASN][1000 genomes]
rs62468380	0.81[ASN][1000 genomes]
rs62468381	0.81[ASN][1000 genomes]
rs62468382	0.83[ASN][1000 genomes]
rs62468385	0.83[ASN][1000 genomes]
rs62468386	0.86[ASN][1000 genomes]
rs62468402	0.89[ASN][1000 genomes]
rs62468403	1.00[AFR][1000 genomes];0.86[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	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
4	nsv831019	chr7:66516808-66720485	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases
5	esv2422035	chr7:66621964-66676630	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1800770	chr7:66629329-66645232	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv1831418	chr7:66629329-66645232	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv1831706	chr7:66629329-66645232	Weak transcription Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv441983	chr7:66629329-66645232	Weak transcription Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12538054	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66621600-66672000	Weak transcription	Fetal Intestine Large	intestine
2	chr7:66628600-66684600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:66629000-66650200	Weak transcription	Fetal Thymus	thymus

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