Variant report

Variant	rs1345107
Chromosome Location	chr10:49794481-49794482
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	chr10:49790222..49791861-chr10:49794010..49795750,2	K562	blood:
2	chr10:49794436..49796437-chr10:49820833..49823076,2	K562	blood:

Variant related genes	Relation type
ENSG00000128805	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1075811	0.83[GIH][hapmap]
rs10857607	0.86[EUR][1000 genomes]
rs11591884	0.88[GIH][hapmap]
rs11592077	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11594078	1.00[CEU][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs12412298	0.86[EUR][1000 genomes]
rs1806438	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1965169	0.87[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2377517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2889659	1.00[MEX][hapmap]
rs3843000	0.86[MEX][hapmap]
rs4572084	0.87[CEU][hapmap]
rs61838376	0.98[EUR][1000 genomes]
rs61838387	0.97[EUR][1000 genomes]
rs61841202	0.85[EUR][1000 genomes]
rs61841203	0.85[EUR][1000 genomes]
rs7079932	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7909968	0.81[CEU][hapmap]
rs935286	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs935291	0.83[GIH][hapmap]

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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv550815	chr10:49774633-49794481	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv550816	chr10:49782417-49794481	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1046588	chr10:49790254-49806169	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1345107	ARHGAP22	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49787800-49796800	Weak transcription	Right Atrium	heart
2	chr10:49788000-49796000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr10:49788200-49795600	Strong transcription	Osteobl	bone
4	chr10:49788200-49795800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr10:49788800-49795000	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr10:49788800-49797200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr10:49790600-49794800	Weak transcription	Brain Hippocampus Middle	brain
8	chr10:49791000-49796200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr10:49791400-49798400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:49792200-49796600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:49792200-49797200	Weak transcription	Brain Anterior Caudate	brain
12	chr10:49792400-49795800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr10:49792400-49795800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:49792400-49796400	Weak transcription	Brain Angular Gyrus	brain
15	chr10:49792600-49795000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr10:49792600-49795200	Weak transcription	NHDF-Ad	bronchial
17	chr10:49792600-49796000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:49792800-49796800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:49792800-49796800	Weak transcription	HUVEC	blood vessel
20	chr10:49793200-49795800	Weak transcription	Left Ventricle	heart
21	chr10:49793400-49794600	ZNF genes & repeats	HSMM	muscle
22	chr10:49793400-49794800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr10:49793600-49795800	Weak transcription	Gastric	stomach
24	chr10:49793800-49795000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr10:49793800-49795600	Strong transcription	NHLF	lung
26	chr10:49794000-49794800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr10:49794000-49795800	Weak transcription	HMEC	breast
28	chr10:49794000-49796600	Weak transcription	HSMMtube	muscle
29	chr10:49794000-49796800	Weak transcription	NH-A	brain
30	chr10:49794200-49795000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr10:49794400-49810600	Enhancers	Brain Substantia Nigra	brain

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