Variant report

Variant	rs12699611
Chromosome Location	chr7:14420512-14420513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1019906	0.81[CEU][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs10245285	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10755842	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs10950520	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11977804	0.82[CEU][hapmap]
rs11983089	0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12155191	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12333379	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12699609	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12699613	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs1319592	0.84[CEU][hapmap];0.80[AMR][1000 genomes]
rs1319593	0.88[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1469618	0.88[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs17168097	0.84[CEU][hapmap]
rs17168106	0.88[CEU][hapmap]
rs17168109	0.80[CEU][hapmap]
rs2116532	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs4141591	0.83[AFR][1000 genomes]
rs4721330	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs4721331	0.80[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6946703	0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6947526	0.81[CEU][hapmap];0.81[CHB][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6958890	0.85[CEU][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs6963946	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs6971911	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949033	chr7:14086106-14860323	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv606281	chr7:14388381-14443963	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
3	esv3400522	chr7:14420243-14420828	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12699611	ARL4A	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:14417600-14420600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:14417600-14421200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:14418000-14420600	Weak transcription	NH-A	brain
4	chr7:14418600-14421200	Weak transcription	HSMM	muscle
5	chr7:14418600-14428400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:14419000-14420600	Weak transcription	Osteobl	bone
7	chr7:14419000-14421000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:14419000-14421200	Weak transcription	NHDF-Ad	bronchial
9	chr7:14419200-14420600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:14420000-14421600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:14420000-14421800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr7:14420400-14421800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:14420400-14422000	Enhancers	NHEK	skin

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