Variant report

Variant	rs617616
Chromosome Location	chr6:164412742-164412743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12191111	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12192423	0.82[EUR][1000 genomes]
rs12200803	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12215299	0.80[EUR][1000 genomes]
rs16895846	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1756	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4499903	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4709030	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4709031	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4709804	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs473823	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs491901	0.88[EUR][1000 genomes]
rs493605	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs526406	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs551475	0.82[EUR][1000 genomes]
rs587114	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs587184	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs616299	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634032	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs656371	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs680187	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs717822	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7451221	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7751193	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs617616	CNO	trans	parietal	SCAN
rs617616	MAP3K4	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164393800-164413800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:164405600-164412800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:164412200-164412800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:164412400-164412800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:164412400-164412800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:164412400-164413000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:164412400-164413000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:164412600-164413600	Weak transcription	Brain Anterior Caudate	brain
9	chr6:164412600-164417600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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