Variant report

Variant	rs4241462
Chromosome Location	chr3:93967206-93967207
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12485419	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12630845	0.86[AMR][1000 genomes]
rs12638900	0.86[AMR][1000 genomes]
rs13079023	0.85[AMR][1000 genomes]
rs1580098	0.86[AMR][1000 genomes]
rs1584929	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1598220	0.81[AMR][1000 genomes]
rs1598223	0.82[AMR][1000 genomes]
rs1598229	0.86[AMR][1000 genomes]
rs1598230	0.86[AMR][1000 genomes]
rs1598234	0.86[AMR][1000 genomes]
rs1609721	0.84[AMR][1000 genomes]
rs2198619	0.86[AMR][1000 genomes]
rs2198620	0.86[AMR][1000 genomes]
rs33970442	0.86[AMR][1000 genomes]
rs34171637	0.87[EUR][1000 genomes]
rs34430074	0.81[AMR][1000 genomes]
rs34757629	0.97[EUR][1000 genomes]
rs34871190	0.81[AMR][1000 genomes]
rs35067079	0.81[AMR][1000 genomes]
rs35648684	0.91[EUR][1000 genomes]
rs35790140	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35797019	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35924628	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4399895	0.86[AMR][1000 genomes]
rs4857267	0.81[EUR][1000 genomes]
rs4857270	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4857289	0.86[AMR][1000 genomes]
rs4857300	0.84[AMR][1000 genomes]
rs62266967	0.90[EUR][1000 genomes]
rs66750406	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67811013	0.86[AMR][1000 genomes]
rs7630241	0.86[AMR][1000 genomes]
rs7633544	0.89[MKK][hapmap]
rs7646963	0.86[AMR][1000 genomes]
rs7653521	0.89[MKK][hapmap]
rs897184	0.86[AMR][1000 genomes]
rs9852322	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv877163	chr3:93795972-94047775	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4241462	ARL6	cis	cerebellum	SCAN
rs4241462	STX19	cis	parietal	SCAN
rs4241462	ARL6	cis	parietal	SCAN
rs4241462	DHFRL1	cis	cerebellum	SCAN
rs4241462	OR5K2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93963600-93968600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:93963800-93968800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:93965200-93969800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:93965800-93967600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:93965800-93968200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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