Variant report

Variant	rs2668746
Chromosome Location	chr15:45615325-45615326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10152337	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10152697	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12324848	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1288861	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16940351	0.91[JPT][hapmap]
rs16941238	1.00[JPT][hapmap]
rs16942066	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1706799	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17533116	0.93[EUR][1000 genomes]
rs17533716	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17535381	0.84[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17537244	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17618294	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2433229	0.83[JPT][hapmap]
rs2433602	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2453546	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2461706	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2486287	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55721266	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55904415	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56267974	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56273246	0.83[ASN][1000 genomes]
rs56306977	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56327050	0.83[ASN][1000 genomes]
rs56937414	0.80[ASN][1000 genomes]
rs56967490	0.83[ASN][1000 genomes]
rs57369693	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57419781	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61301536	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72709081	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72709084	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72709088	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72711253	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711255	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711259	0.83[ASN][1000 genomes]
rs9972405	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9972498	0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9972528	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv977713	chr15:45611707-45620772	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2668746	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45612000-45615600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:45612400-45615600	Weak transcription	Gastric	stomach
3	chr15:45613000-45615600	Weak transcription	Stomach Mucosa	stomach
4	chr15:45613600-45622000	Weak transcription	Pancreas	Pancrea
5	chr15:45613800-45618200	Weak transcription	Fetal Brain Male	brain
6	chr15:45614200-45616000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr15:45614200-45619000	Weak transcription	Fetal Brain Female	brain

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