Variant report

Variant	rs2315020
Chromosome Location	chr17:38827666-38827667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38800703..38802549-chr17:38827643..38829167,2	MCF-7	breast:
2	chr17:38822001..38824383-chr17:38827508..38829581,2	K562	blood:

Variant related genes	Relation type
ENSG00000073584	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1029792	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1048572	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1048573	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12943859	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2008469	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2014704	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2109223	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2159430	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2253717	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2429549	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2462962	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462963	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462964	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462970	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2469818	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3752026	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4890093	0.86[EUR][1000 genomes]
rs4890119	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6503547	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6503549	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7209467	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7209735	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7210983	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7212255	0.87[ASN][1000 genomes]
rs7219483	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7223332	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7223354	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs726848	0.87[ASN][1000 genomes]
rs758630	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8068721	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8076587	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs917593	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs917595	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9896791	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9900324	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9906785	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9915135	0.91[EUR][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	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2315020	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs2315020	KRT222	cis	Nerve Tibial	GTEx
rs2315020	KRT24	cis	Esophagus Mucosa	GTEx
rs2315020	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38827200-38827800	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr17:38827200-38828000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:38827200-38828200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr17:38827600-38828000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr17:38827600-38828000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr17:38827600-38828200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:38827600-38828200	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr17:38827600-38828200	Enhancers	Spleen	Spleen

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