Variant report

Variant	rs1381065
Chromosome Location	chr3:115869444-115869445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10804521	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10804522	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12485667	0.84[ASN][1000 genomes]
rs12486465	0.84[ASN][1000 genomes]
rs12488904	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12496701	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs1461110	0.89[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1461112	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461113	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461117	0.84[ASN][1000 genomes]
rs1461138	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1563933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16824478	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs16824491	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16824495	0.84[ASN][1000 genomes]
rs17359	0.84[ASN][1000 genomes]
rs17631108	0.94[ASN][1000 genomes]
rs17643878	0.84[ASN][1000 genomes]
rs17698500	0.89[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs17699134	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]
rs1882012	0.83[CEU][hapmap]
rs1920363	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs1920365	1.00[ASN][1000 genomes]
rs1920367	1.00[ASN][1000 genomes]
rs1920370	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1920374	0.82[CEU][hapmap]
rs1920375	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920376	0.82[CEU][hapmap]
rs1950085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141628	0.99[ASN][1000 genomes]
rs34424845	0.84[ASN][1000 genomes]
rs41456847	0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs4146782	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4261878	1.00[ASN][1000 genomes]
rs4511899	0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs4560296	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56357456	0.84[EUR][1000 genomes]
rs57196061	1.00[ASN][1000 genomes]
rs57425502	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62269187	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62269188	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62269190	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67278926	0.83[ASN][1000 genomes]
rs67551037	0.84[ASN][1000 genomes]
rs6764630	0.83[CEU][hapmap]
rs6779886	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs67853012	0.84[ASN][1000 genomes]
rs6787788	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs73140910	0.94[ASN][1000 genomes]
rs73140911	0.94[ASN][1000 genomes]
rs73140912	0.94[ASN][1000 genomes]
rs73140913	0.94[ASN][1000 genomes]
rs73140921	1.00[ASN][1000 genomes]
rs7428913	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7614089	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7639609	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872625	0.87[CEU][hapmap]
rs9875743	0.83[CEU][hapmap]
rs9878125	0.87[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
rs1381065	ARHGAP44	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115866800-115871600	Enhancers	Brain Germinal Matrix	brain
2	chr3:115867200-115869800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:115867200-115870200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:115867200-115870200	Enhancers	Brain Angular Gyrus	brain
5	chr3:115867400-115869600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:115867600-115869800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:115867600-115870200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:115867800-115870400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:115868400-115872000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:115868600-115879600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:115868800-115872000	Weak transcription	Fetal Lung	lung
12	chr3:115869000-115869600	Enhancers	Brain Anterior Caudate	brain
13	chr3:115869000-115870000	Weak transcription	Brain Substantia Nigra	brain
14	chr3:115869000-115880000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:115869200-115869600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:115869200-115869800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:115869200-115871200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:115869200-115871600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:115869400-115874800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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