Variant report

Variant	rs4664689
Chromosome Location	chr2:151482490-151482491
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	chr2:151471840..151473581-chr2:151481556..151483221,2	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10188741	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10432416	0.98[ASN][1000 genomes]
rs10497064	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497067	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10497068	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10497069	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10803803	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10930181	0.85[AFR][1000 genomes]
rs10930198	0.90[ASN][1000 genomes]
rs10930203	0.98[ASN][1000 genomes]
rs11894862	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11899711	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12052383	0.90[CHB][hapmap]
rs12473120	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614085	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13019271	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16828368	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs16828372	0.90[CHB][hapmap]
rs2247416	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290815	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290816	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290817	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2341059	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341060	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341063	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341067	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341071	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341072	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2341073	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341074	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341075	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2341078	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341081	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341082	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341083	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341084	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341085	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341086	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341087	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341088	0.98[ASN][1000 genomes]
rs2341089	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341090	0.98[ASN][1000 genomes]
rs2341091	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2879931	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879932	0.85[AFR][1000 genomes]
rs4233665	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233666	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233667	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4297879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334493	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4365460	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374370	0.91[AFR][1000 genomes]
rs4380232	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4408725	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514872	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530365	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530366	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4600650	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627564	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4664150	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664692	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710003	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6724645	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71338158	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557930	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559963	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7560326	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562436	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569499	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593427	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597424	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602198	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287861	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287862	0.85[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
rs4664689	ARL5A	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151473000-151487000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:151476800-151483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:151476800-151485200	Weak transcription	Psoas Muscle	Psoas
4	chr2:151478800-151485200	Weak transcription	Aorta	Aorta
5	chr2:151479200-151483000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:151479400-151482800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:151480000-151484600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:151480000-151485600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:151480400-151485200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:151480800-151482600	Enhancers	Hela-S3	cervix
11	chr2:151480800-151483600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:151480800-151487200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:151481000-151483400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:151481000-151483400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:151481000-151483600	Weak transcription	Adipose Nuclei	Adipose
16	chr2:151481000-151487400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:151481200-151482800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:151481200-151483400	Weak transcription	Osteobl	bone
19	chr2:151481400-151483000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:151481400-151483600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:151481600-151483200	Weak transcription	NHDF-Ad	bronchial
22	chr2:151482000-151482600	Weak transcription	HSMMtube	muscle
23	chr2:151482000-151482600	Enhancers	NHEK	skin
24	chr2:151482000-151482800	Weak transcription	HSMM	muscle
25	chr2:151482000-151487000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:151482000-151487200	Weak transcription	NH-A	brain
27	chr2:151482000-151487200	Weak transcription	NHLF	lung
28	chr2:151482200-151483200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:151482400-151483600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:151482400-151483800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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