Variant report

Variant	rs2590816
Chromosome Location	chr4:54485327-54485328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54484339..54487023-chr4:54487533..54490368,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1079230	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1107027	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1477875	0.96[ASN][1000 genomes]
rs1477876	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1546526	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1972815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996005	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2164266	0.91[ASN][1000 genomes]
rs2572283	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2572291	0.96[ASN][1000 genomes]
rs2572299	0.96[ASN][1000 genomes]
rs2590780	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2590781	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2590823	0.87[EUR][1000 genomes]
rs2616386	0.89[CEU][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2616410	0.85[EUR][1000 genomes]
rs2668516	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668521	0.96[ASN][1000 genomes]
rs2668524	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2668529	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2668548	0.86[EUR][1000 genomes]
rs2668549	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2668557	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2668566	0.88[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7686480	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs907510	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1004253	chr4:54471388-54494983	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1010881	chr4:54471545-54494983	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2590816	TXNDC9	cis	parietal	SCAN
rs2590816	FIP1L1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54484800-54487800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:54485200-54505800	Weak transcription	Esophagus	oesophagus

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