Variant report

Variant	rs7305391
Chromosome Location	chr12:58007678-58007679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT5A	chr12:58007638-58008127	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr12:58007593-58008207	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57911754..57916322-chr12:58006406..58010716,5	K562	blood:
2	chr12:57854178..57856393-chr12:58005789..58008256,3	K562	blood:
3	chr12:58004618..58008024-chr12:58024930..58028098,5	MCF-7	breast:
4	chr12:58007372..58011848-chr12:58013286..58019253,6	MCF-7	breast:
5	chr12:57892478..57894740-chr12:58006142..58008775,2	MCF-7	breast:
6	chr12:57911699..57918406-chr12:58000825..58010019,18	K562	blood:
7	chr12:58002964..58008004-chr12:58117447..58122099,5	MCF-7	breast:
8	chr12:58004396..58008788-chr12:58163385..58167140,4	MCF-7	breast:

No data

Variant related genes	Relation type
ARHGEF25	TF binding region
ENSG00000166986	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000224713	Chromatin interaction
ENSG00000135454	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000111087	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11172262	0.88[EUR][1000 genomes]
rs11613457	1.00[YRI][hapmap]
rs11614506	1.00[YRI][hapmap]
rs1806652	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs28382838	1.00[YRI][hapmap]
rs34181394	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60586224	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314872	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964896	0.85[EUR][1000 genomes]
rs812315	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs8873	0.80[CEU][hapmap]

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	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7305391	AC025165.8	cis	Nerve Tibial	GTEx
rs7305391	ARHGEF25	cis	Nerve Tibial	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58005600-58008000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
2	chr12:58005600-58011400	Weak transcription	Lung	lung
3	chr12:58005600-58013200	Weak transcription	Gastric	stomach
4	chr12:58005800-58008400	Weak transcription	Aorta	Aorta
5	chr12:58006000-58010000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
6	chr12:58006200-58008000	Genic enhancers	Fetal Stomach	stomach
7	chr12:58006200-58008000	Enhancers	HepG2	liver
8	chr12:58006200-58008200	Enhancers	Right Atrium	heart
9	chr12:58006200-58008600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr12:58006200-58010000	Weak transcription	Brain Substantia Nigra	brain
11	chr12:58006200-58010200	Weak transcription	NHDF-Ad	bronchial
12	chr12:58006200-58010400	Weak transcription	NH-A	brain
13	chr12:58006200-58014800	Weak transcription	Brain Angular Gyrus	brain
14	chr12:58006400-58007800	Bivalent Enhancer	Rectal Smooth Muscle	rectum
15	chr12:58006400-58007800	Weak transcription	A549	lung
16	chr12:58006400-58008000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:58006400-58008400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:58006400-58008600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:58006400-58009000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:58006400-58009000	Weak transcription	Brain Anterior Caudate	brain
21	chr12:58006400-58009000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:58006400-58009400	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:58006400-58011200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:58006600-58008000	Weak transcription	Brain Germinal Matrix	brain
25	chr12:58006600-58009400	Weak transcription	NHLF	lung
26	chr12:58006600-58010000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr12:58006600-58011000	Strong transcription	Fetal Lung	lung
28	chr12:58006600-58013200	Weak transcription	Pancreas	Pancrea
29	chr12:58006800-58008400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:58006800-58008600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
31	chr12:58006800-58009200	Genic enhancers	Colon Smooth Muscle	Colon
32	chr12:58006800-58010200	Weak transcription	Fetal Brain Male	brain
33	chr12:58006800-58011400	Strong transcription	Ovary	ovary
34	chr12:58006800-58011600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:58006800-58011600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:58006800-58011600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:58006800-58011800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:58006800-58012000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:58007000-58008600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:58007000-58009200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
41	chr12:58007000-58009600	Genic enhancers	Fetal Muscle Leg	muscle
42	chr12:58007000-58012000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:58007200-58007800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:58007200-58007800	Enhancers	Fetal Heart	heart
45	chr12:58007200-58008200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:58007200-58008600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:58007200-58008600	Enhancers	Spleen	Spleen
48	chr12:58007200-58009400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:58007200-58009800	Strong transcription	Osteobl	bone
50	chr12:58007200-58011200	Strong transcription	Fetal Brain Female	brain

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