Variant report

Variant	rs12211928
Chromosome Location	chr6:114412037-114412038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10782177	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1157989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11967410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970460	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12190983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12201726	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12201804	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12203341	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12207338	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12213853	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191369	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1961955	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2475621	0.81[CEU][hapmap]
rs2475623	0.80[CEU][hapmap]
rs2475624	0.81[CEU][hapmap]
rs4551200	0.81[CEU][hapmap]
rs62418080	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7742134	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[ASN][1000 genomes]
rs7743208	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7753206	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7764690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374432	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs9398370	0.81[CEU][hapmap]
rs9481418	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481421	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9488328	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9488329	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9488334	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12211928	BET3L	cis	parietal	SCAN
rs12211928	ROS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114385600-114415800	Weak transcription	HSMM	muscle
2	chr6:114402400-114417800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:114409200-114421600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:114411000-114413600	Enhancers	Brain Hippocampus Middle	brain
5	chr6:114411200-114413200	Enhancers	Brain Cingulate Gyrus	brain
6	chr6:114411200-114413600	Enhancers	Brain Substantia Nigra	brain
7	chr6:114411400-114413800	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr6:114411600-114412200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:114411600-114412200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:114411600-114412400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:114411600-114413200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:114411600-114413400	Enhancers	Brain Angular Gyrus	brain
13	chr6:114411800-114412400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:114411800-114412400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:114411800-114412600	Enhancers	HSMMtube	muscle
16	chr6:114411800-114418000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:114412000-114413400	Enhancers	Brain Anterior Caudate	brain
18	chr6:114412000-114414200	Weak transcription	H9 Cell Line	embryonic stem cell

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