Variant report

Variant	rs1363213
Chromosome Location	chr5:108591363-108591364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11739672	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741980	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11743452	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744353	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746207	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748450	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749718	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1363212	0.98[ASN][1000 genomes]
rs1592807	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1592810	0.91[ASN][1000 genomes]
rs1592811	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161655	0.93[ASN][1000 genomes]
rs17161659	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17161665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161674	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1807818	0.87[AFR][1000 genomes]
rs1833567	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1833568	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1833569	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862201	1.00[ASN][1000 genomes]
rs1862202	1.00[ASN][1000 genomes]
rs1862203	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895200	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895201	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2011638	0.85[AFR][1000 genomes]
rs2080858	0.85[ASN][1000 genomes]
rs35812497	0.84[ASN][1000 genomes]
rs36123121	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4388251	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4388252	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4392675	1.00[ASN][1000 genomes]
rs4438924	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4541698	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57629433	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60335509	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60878839	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60905342	0.83[ASN][1000 genomes]
rs61701247	0.93[ASN][1000 genomes]
rs6594365	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6863688	1.00[ASN][1000 genomes]
rs6863893	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879134	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7700458	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704359	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705919	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721272	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721427	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721730	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721870	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722100	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027163	chr5:108445447-108839913	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv599338	chr5:108528729-108675737	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv4955	chr5:108577946-108611852	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv508375	chr5:108587628-108624046	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1363213	PJA2	cis	cerebellum	SCAN
rs1363213	EFNA5	cis	cerebellum	SCAN
rs1363213	RHPN1	trans	brain	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108586000-108606000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:108588800-108594000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:108589000-108592000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:108589600-108592600	Enhancers	Cortex derived primary cultured neurospheres	brain

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