Variant report

Variant	rs4408725
Chromosome Location	chr2:151498770-151498771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10186504	0.94[AFR][1000 genomes]
rs10188741	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10201751	0.94[AFR][1000 genomes]
rs10432416	0.98[ASN][1000 genomes]
rs10497064	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497067	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10497068	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10497069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10803803	1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10930198	0.90[ASN][1000 genomes]
rs10930203	0.98[ASN][1000 genomes]
rs11894862	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11899711	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12052383	0.81[CHB][hapmap]
rs12473120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614085	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13019271	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16828368	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs2247416	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290815	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290816	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290817	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2341059	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341060	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341061	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341062	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341063	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341064	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341065	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341066	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341067	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341068	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341071	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341072	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2341073	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341074	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341075	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2341078	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341081	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341082	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341084	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341088	0.98[ASN][1000 genomes]
rs2341089	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341090	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341091	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2879931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879932	1.00[AFR][1000 genomes]
rs4233665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4297879	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334493	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4365460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4380232	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514872	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4600650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627564	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4664150	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664689	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664692	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710003	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6724645	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71338158	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559963	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7560326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562436	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593427	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287862	1.00[AFR][1000 genomes];0.98[ASN][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	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv532473	chr2:151164210-151701860	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv834415	chr2:151374254-151558649	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv2757836	chr2:151457277-151844210	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv2759096	chr2:151457277-151844210	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4408725	ARL5A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151494600-151504600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:151496800-151500600	Weak transcription	Fetal Stomach	stomach
3	chr2:151497000-151498800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:151497000-151500000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:151497000-151500200	Weak transcription	A549	lung
6	chr2:151497000-151500600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:151497000-151501400	Weak transcription	Fetal Lung	lung
8	chr2:151497200-151499600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:151497200-151499800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:151497200-151499800	Weak transcription	HSMM	muscle
11	chr2:151497200-151499800	Weak transcription	NHDF-Ad	bronchial
12	chr2:151497200-151500000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:151497200-151500000	Weak transcription	NHLF	lung
14	chr2:151497200-151500200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:151497200-151500400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:151497200-151500400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:151497200-151500800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:151497800-151499600	Weak transcription	Osteobl	bone
19	chr2:151498200-151499000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links