Variant report

Variant	rs16828577
Chromosome Location	chr2:151538472-151538473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:151527893..151530038-chr2:151538042..151540023,2	K562	blood:
2	chr2:151533248..151535265-chr2:151536631..151538715,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10186504	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10188741	0.89[EUR][1000 genomes]
rs10196763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10201751	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10432416	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10497067	0.89[EUR][1000 genomes]
rs10497068	0.89[EUR][1000 genomes]
rs10803803	0.89[EUR][1000 genomes]
rs10930198	0.81[EUR][1000 genomes]
rs10930203	0.89[EUR][1000 genomes]
rs11894862	0.89[EUR][1000 genomes]
rs11899711	0.89[EUR][1000 genomes]
rs12614085	0.89[EUR][1000 genomes]
rs13019271	0.89[EUR][1000 genomes]
rs13409790	0.87[AMR][1000 genomes]
rs13416697	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13421850	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13428302	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13430342	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1519782	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341059	0.86[TSI][hapmap]
rs2341088	0.89[EUR][1000 genomes]
rs2341089	0.89[EUR][1000 genomes]
rs2341090	0.89[EUR][1000 genomes]
rs2341091	0.89[EUR][1000 genomes]
rs2879932	0.89[EUR][1000 genomes]
rs4297879	0.86[TSI][hapmap]
rs4627564	0.95[ASN][1000 genomes]
rs4664689	0.86[TSI][hapmap]
rs6710003	0.89[EUR][1000 genomes]
rs9287862	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	esv2756950	chr2:151502539-151749973	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv834416	chr2:151517784-151699912	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1010993	chr2:151535786-151742522	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16828577	ARL5A	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151534400-151557800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:151535000-151539600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:151535200-151539600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:151535400-151539400	Enhancers	Osteobl	bone
5	chr2:151535800-151539400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr2:151535800-151539400	Enhancers	NHDF-Ad	bronchial
7	chr2:151536000-151539400	Enhancers	Hela-S3	cervix
8	chr2:151536600-151539400	Enhancers	NHLF	lung
9	chr2:151536800-151539400	Enhancers	Fetal Intestine Large	intestine
10	chr2:151536800-151539600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:151537400-151538800	Enhancers	HUVEC	blood vessel
12	chr2:151537400-151539200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:151538000-151538800	Enhancers	NH-A	brain
14	chr2:151538200-151538600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:151538200-151538600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:151538200-151539200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:151538200-151539200	Weak transcription	HSMM	muscle
18	chr2:151538400-151539200	Enhancers	Fetal Intestine Small	intestine

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