Variant report

Variant	rs17046025
Chromosome Location	chr4:166066606-166066607
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10000910	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014286	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723353	0.87[AFR][1000 genomes]
rs17008146	0.93[LWK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs17046008	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17046026	0.96[AFR][1000 genomes]
rs28408505	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28415222	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691153	0.83[GIH][hapmap]
rs4691154	0.83[GIH][hapmap]
rs4691164	0.82[JPT][hapmap]
rs4691165	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4691169	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59951611	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60474827	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62352255	0.84[ASN][1000 genomes]
rs6536897	0.83[ASW][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs67185057	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6821879	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822635	0.86[JPT][hapmap]
rs6844945	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72991905	0.87[AFR][1000 genomes]
rs7683597	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][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	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv881168	chr4:165975122-166196438	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17046025	TMEM30B	trans	brain	seeQTL
rs17046025	COL6A2	trans	brain	seeQTL
rs17046025	PRG4	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166066400-166071200	Weak transcription	Liver	Liver
2	chr4:166066600-166071600	Weak transcription	HepG2	liver

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