Variant report

Variant	rs520026
Chromosome Location	chr13:54761394-54761395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1537644	0.88[ASN][1000 genomes]
rs2260462	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2261357	0.86[JPT][hapmap]
rs2261359	0.86[JPT][hapmap]
rs2261365	0.86[JPT][hapmap]
rs2576113	0.93[EUR][1000 genomes]
rs2576118	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2576132	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2576143	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2576144	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2782515	0.93[EUR][1000 genomes]
rs2782517	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2782518	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2784552	0.86[JPT][hapmap]
rs2784558	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs484366	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs515604	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs518647	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs538663	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs564930	0.86[ASN][1000 genomes]
rs574751	0.93[EUR][1000 genomes]
rs632059	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs636911	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs653228	0.81[AFR][1000 genomes]
rs664745	0.93[EUR][1000 genomes]
rs681748	0.93[EUR][1000 genomes]
rs688466	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs795635	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs795642	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs795643	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs795652	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs795653	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs795655	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs795656	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs797060	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7993452	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs812128	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3375545	chr13:54517432-54908108	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv561701	chr13:54711276-54826104	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs520026	COL9A3	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54759600-54763400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr13:54760200-54768000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr13:54760400-54763600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr13:54760400-54770200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:54760600-54763200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr13:54760600-54763400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr13:54760600-54763800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:54760600-54768200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:54760800-54766600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr13:54761000-54763800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr13:54761000-54763800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr13:54761200-54763400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr13:54761200-54763400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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