Variant report

Variant	rs7984469
Chromosome Location	chr13:55222298-55222299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10220066	0.82[EUR][1000 genomes]
rs12871538	0.90[EUR][1000 genomes]
rs12872969	0.90[EUR][1000 genomes]
rs1351172	0.85[EUR][1000 genomes]
rs1478654	0.87[EUR][1000 genomes]
rs1478655	0.87[EUR][1000 genomes]
rs1478656	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes]
rs1478657	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes]
rs1478658	0.90[EUR][1000 genomes]
rs17618437	0.90[EUR][1000 genomes]
rs1904216	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34196302	1.00[EUR][1000 genomes]
rs35278435	0.83[EUR][1000 genomes]
rs7984619	1.00[EUR][1000 genomes]
rs7993123	1.00[EUR][1000 genomes]
rs7999254	0.82[EUR][1000 genomes]
rs9316740	0.83[ASN][1000 genomes]
rs9527234	0.87[EUR][1000 genomes]
rs9527238	0.90[EUR][1000 genomes]
rs9536773	0.82[EUR][1000 genomes]
rs9536777	0.87[EUR][1000 genomes]
rs9536780	0.87[EUR][1000 genomes]
rs9536781	0.87[EUR][1000 genomes]
rs9536783	0.89[EUR][1000 genomes]
rs9536784	0.88[EUR][1000 genomes]
rs9536785	0.90[EUR][1000 genomes]
rs9536786	0.90[EUR][1000 genomes]
rs9536787	0.90[EUR][1000 genomes]
rs9536788	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs9536789	0.88[EUR][1000 genomes]
rs9536791	1.00[EUR][1000 genomes]
rs9536793	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9536794	0.98[EUR][1000 genomes]
rs9536796	1.00[EUR][1000 genomes]
rs9591609	0.85[EUR][1000 genomes]
rs9591613	0.90[EUR][1000 genomes]
rs9591614	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591615	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9597013	0.83[EUR][1000 genomes]
rs9597016	0.87[EUR][1000 genomes]
rs9597017	0.87[EUR][1000 genomes]
rs9597023	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9597024	1.00[EUR][1000 genomes]
rs9597026	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9597027	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9597032	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349795	chr13:54892694-55252030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv917186	chr13:55022134-55433232	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv561702	chr13:55086271-55808127	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1043044	chr13:55102831-55285581	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1048599	chr13:55143426-55476042	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1051640	chr13:55143426-55478547	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv561703	chr13:55143754-55473732	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv916104	chr13:55154006-55433232	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1052745	chr13:55159674-55459161	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv541779	chr13:55159674-55459161	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7984469	C13orf1	cis	parietal	SCAN
rs7984469	ARL11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:55218400-55224000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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