Variant report

Variant	rs12530782
Chromosome Location	chr7:66715365-66715366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11971398	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12532995	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs12535651	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537561	1.00[AFR][1000 genomes]
rs12537954	1.00[AFR][1000 genomes]
rs12540794	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17144570	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4717359	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4718480	0.88[AMR][1000 genomes]
rs62464976	0.88[AMR][1000 genomes]
rs62465000	1.00[AFR][1000 genomes]
rs62465002	1.00[AFR][1000 genomes]
rs62465005	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs62465011	0.84[AMR][1000 genomes]
rs62465013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465017	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62465037	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62465038	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62465040	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62465044	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1032237	chr7:66644492-66785029	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv970518	chr7:66647675-66742783	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12530782	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66667800-66738400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:66685000-66717000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr7:66688800-66716600	Weak transcription	Fetal Intestine Large	intestine
4	chr7:66691600-66716400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:66691800-66716200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:66691800-66716400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:66694400-66715600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:66694800-66766600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:66695000-66716000	Weak transcription	Liver	Liver
10	chr7:66696000-66716800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:66698200-66717000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:66698800-66716400	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:66701600-66766600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:66705000-66724400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:66705400-66716200	Weak transcription	Fetal Stomach	stomach
16	chr7:66707000-66717000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr7:66711200-66716400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:66714400-66715800	Enhancers	NHEK	skin
19	chr7:66714600-66716000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr7:66715000-66717000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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