Variant report

Variant	rs17699134
Chromosome Location	chr3:115885360-115885361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10804521	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10804522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12485667	0.95[ASN][1000 genomes]
rs12486465	0.95[ASN][1000 genomes]
rs12488904	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12496701	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs1381065	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1461110	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1461112	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1461113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1461115	0.82[ASN][1000 genomes]
rs1461117	0.95[ASN][1000 genomes]
rs1461138	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1563933	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16824478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16824491	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16824495	0.95[ASN][1000 genomes]
rs17359	0.95[ASN][1000 genomes]
rs17631108	0.84[ASN][1000 genomes]
rs17643878	0.95[ASN][1000 genomes]
rs17698500	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1920363	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1920365	0.90[ASN][1000 genomes]
rs1920367	0.90[ASN][1000 genomes]
rs1920370	0.91[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs1920375	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs1920376	0.82[CEU][hapmap]
rs1950085	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2141628	0.88[ASN][1000 genomes]
rs34424845	0.95[ASN][1000 genomes]
rs41456847	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4146782	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4261878	0.90[ASN][1000 genomes]
rs4511899	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4560296	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56357456	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57196061	0.90[ASN][1000 genomes]
rs57425502	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62269187	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62269188	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62269190	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67278926	0.93[ASN][1000 genomes]
rs67551037	0.95[ASN][1000 genomes]
rs6779886	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs67853012	0.95[ASN][1000 genomes]
rs6787788	0.86[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73140910	0.84[ASN][1000 genomes]
rs73140911	0.84[ASN][1000 genomes]
rs73140912	0.84[ASN][1000 genomes]
rs73140913	0.84[ASN][1000 genomes]
rs73140921	0.90[ASN][1000 genomes]
rs73140968	0.87[ASN][1000 genomes]
rs7428913	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7614089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7639609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9872625	0.82[CEU][hapmap]
rs9878125	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2756413	chr3:115721898-115908480	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2751975	chr3:115766285-115902901	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2755046	chr3:115818840-115942952	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv591345	chr3:115819376-115902901	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2752728	chr3:115833212-115902901	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2751976	chr3:115867310-115903310	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17699134	ARHGAP44	trans	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115881000-115889600	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:115881600-115891800	Weak transcription	Fetal Brain Male	brain
3	chr3:115883000-115885600	Enhancers	Brain Substantia Nigra	brain
4	chr3:115883600-115885400	Enhancers	Brain Angular Gyrus	brain
5	chr3:115883600-115885400	Enhancers	Brain Anterior Caudate	brain
6	chr3:115883600-115885400	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:115883600-115885400	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr3:115883800-115885400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:115884000-115885400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:115884000-115885400	Enhancers	Brain Hippocampus Middle	brain
11	chr3:115884000-115885400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:115884400-115886800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:115884800-115886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:115885000-115886000	Weak transcription	Brain Germinal Matrix	brain

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