Variant report

Variant	rs12614085
Chromosome Location	chr2:151501545-151501546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10186504	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10188741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196763	0.89[EUR][1000 genomes]
rs10201751	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10432416	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497064	0.98[ASN][1000 genomes]
rs10497067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497069	1.00[AFR][1000 genomes]
rs10803803	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10930198	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10930203	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052383	0.81[CHB][hapmap]
rs12473120	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13019271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416697	0.90[EUR][1000 genomes]
rs13421850	0.90[EUR][1000 genomes]
rs13430342	0.90[EUR][1000 genomes]
rs1519782	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16828368	0.81[CHB][hapmap]
rs16828577	0.89[EUR][1000 genomes]
rs2247416	0.98[ASN][1000 genomes]
rs2290815	0.98[ASN][1000 genomes]
rs2290816	0.98[ASN][1000 genomes]
rs2341059	0.81[CHB][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.80[ASN][1000 genomes]
rs2341060	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341061	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341062	0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[ASN][1000 genomes]
rs2341063	0.98[ASN][1000 genomes]
rs2341064	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2341065	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2341066	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2341067	0.95[ASN][1000 genomes]
rs2341068	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2341071	0.98[ASN][1000 genomes]
rs2341072	0.93[ASN][1000 genomes]
rs2341073	0.95[ASN][1000 genomes]
rs2341074	0.98[ASN][1000 genomes]
rs2341075	0.93[ASN][1000 genomes]
rs2341078	0.98[ASN][1000 genomes]
rs2341081	0.98[ASN][1000 genomes]
rs2341082	0.98[ASN][1000 genomes]
rs2341083	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341084	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341085	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341086	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341087	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341088	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341090	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879931	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2879932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4233665	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4233666	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4233667	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4297879	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.98[ASN][1000 genomes]
rs4334493	0.81[CHB][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4365460	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4380232	0.98[ASN][1000 genomes]
rs4408725	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4514872	0.98[ASN][1000 genomes]
rs4530365	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4530366	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4600650	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4627564	0.94[AFR][1000 genomes]
rs4664150	0.98[ASN][1000 genomes]
rs4664689	1.00[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4664692	0.98[ASN][1000 genomes]
rs6710003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71338158	0.81[ASN][1000 genomes]
rs7557930	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7559963	0.82[ASN][1000 genomes]
rs7560326	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7562436	0.98[ASN][1000 genomes]
rs7569499	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7593427	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7597424	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7602198	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9287861	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9287862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs12614085	ARL5A	cis	cerebellum	SCAN

Chromatin state (count:28 , 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	chr2:151499000-151501800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr2:151499000-151503600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:151499600-151501600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:151499600-151501600	Enhancers	HMEC	breast
6	chr2:151499600-151502000	Enhancers	NH-A	brain
7	chr2:151499600-151502200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:151499800-151502000	Enhancers	HSMM	muscle
9	chr2:151499800-151502800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:151500000-151502000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:151500000-151502200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr2:151500000-151502200	Enhancers	NHLF	lung
13	chr2:151500000-151502400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:151500200-151502000	Enhancers	HSMMtube	muscle
15	chr2:151500200-151502400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:151500400-151501600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:151500400-151502600	Enhancers	Osteobl	bone
18	chr2:151500600-151501600	Enhancers	Brain Substantia Nigra	brain
19	chr2:151500600-151501600	Enhancers	Fetal Stomach	stomach
20	chr2:151500600-151501600	Enhancers	A549	lung
21	chr2:151500600-151502200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:151500600-151502400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:151500800-151502200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:151500800-151502600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:151501000-151503800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:151501400-151501600	Enhancers	Fetal Lung	lung
27	chr2:151501400-151501800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:151501400-151502400	Enhancers	NHDF-Ad	bronchial

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