Variant report

Variant	rs56174213
Chromosome Location	chr5:98290136-98290137
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98261995..98270397-chr5:98280624..98292060,15	K562	blood:
2	chr5:98262437..98267686-chr5:98287585..98292205,9	K562	blood:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction
ENSG00000153922	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs41300817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41300819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55677526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55693839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55704716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55769608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55845744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55877450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55899721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55905355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55914571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55932002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55976246	1.00[AFR][1000 genomes]
rs56017435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56053751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56100354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56133601	1.00[AFR][1000 genomes]
rs56197564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56262721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56321645	1.00[AFR][1000 genomes]
rs56328362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56365720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56381912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7701147	1.00[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	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56174213	GSTO1	trans	lymphoblastoid	RTeQTL
rs56174213	CDC27	trans	lymphoblastoid	RTeQTL
rs56174213	WWC3	trans	lymphoblastoid	RTeQTL
rs56174213	TRAP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
2	chr5:98274800-98297200	Weak transcription	Thymus	Thymus
3	chr5:98278600-98299400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:98279400-98298400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:98282600-98290400	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:98283800-98293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:98289400-98290400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:98290000-98290800	Flanking Active TSS	K562	blood

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