Variant report

Variant	rs17601275
Chromosome Location	chr13:52454393-52454394
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1748124	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1886322	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4310756	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4375566	0.85[ASN][1000 genomes]
rs4943040	0.86[MKK][hapmap]
rs7325195	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7326982	0.81[ASN][1000 genomes]
rs7490241	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs932914	0.85[CEU][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9526802	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526803	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535776	0.84[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs9535779	0.96[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535780	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535781	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535782	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535783	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535786	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9596596	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs9596598	0.86[JPT][hapmap]
rs9634848	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17601275	LOC440138	cis	multi-tissue	Pritchard
rs17601275	NCRNA00282	cis	cerebellum	SCAN
rs17601275	VPS36	cis	cerebellum	SCAN
rs17601275	WDFY2	cis	cerebellum	SCAN
rs17601275	CKAP2	cis	cerebellum	SCAN
rs17601275	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs17601275	ATP7B	cis	lymphoblastoid	seeQTL
rs17601275	CKAP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52433800-52479400	Weak transcription	HepG2	liver
2	chr13:52438200-52455400	Weak transcription	Fetal Intestine Small	intestine
3	chr13:52446200-52457000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:52448200-52457000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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