Variant report

Variant	rs412729
Chromosome Location	chr6:164444005-164444006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs105481	0.80[EUR][1000 genomes]
rs189976	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs189977	0.80[EUR][1000 genomes]
rs189978	0.81[EUR][1000 genomes]
rs205986	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs205988	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs205989	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205991	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs206006	0.80[EUR][1000 genomes]
rs206007	0.80[EUR][1000 genomes]
rs206008	0.80[EUR][1000 genomes]
rs206009	0.80[EUR][1000 genomes]
rs206012	0.80[EUR][1000 genomes]
rs206013	0.81[EUR][1000 genomes]
rs34113046	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373265	0.82[EUR][1000 genomes]
rs374714	0.82[EUR][1000 genomes]
rs375691	0.82[EUR][1000 genomes]
rs386383	0.82[EUR][1000 genomes]
rs388305	0.82[EUR][1000 genomes]
rs448500	0.82[EUR][1000 genomes]
rs4709808	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4709809	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4709812	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4709813	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4709814	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs85750	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs85751	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9355452	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1026707	chr6:164188210-164749206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv538527	chr6:164188210-164749206	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830858	chr6:164296054-164455743	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1019703	chr6:164424683-164488780	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv1796945	chr6:164430826-164448156	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs412729	QKI	cis	cerebellum	SCAN
rs412729	SLC22A3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164439200-164444600	Weak transcription	Fetal Heart	heart
2	chr6:164442200-164446400	Enhancers	Fetal Muscle Leg	muscle
3	chr6:164442600-164444200	Enhancers	Adipose Nuclei	Adipose
4	chr6:164442800-164444400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:164442800-164444400	Enhancers	Brain Germinal Matrix	brain
6	chr6:164442800-164444400	Enhancers	Fetal Muscle Trunk	muscle
7	chr6:164442800-164444600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:164443000-164444200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:164443000-164446000	Weak transcription	Right Atrium	heart
10	chr6:164443200-164459000	Weak transcription	Spleen	Spleen
11	chr6:164443400-164445000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr6:164443400-164447000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:164443400-164447200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:164443800-164444200	Enhancers	Brain Anterior Caudate	brain
15	chr6:164444000-164444400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:164444000-164445000	Weak transcription	Psoas Muscle	Psoas
17	chr6:164444000-164445000	Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr6:164444000-164447400	Weak transcription	Fetal Brain Male	brain

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