Variant report

Variant	rs16942066
Chromosome Location	chr15:45638247-45638248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10152337	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10152697	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10851425	1.00[CHB][hapmap]
rs1153830	0.88[CHB][hapmap]
rs1153831	0.88[CHB][hapmap]
rs1153832	0.88[CHB][hapmap]
rs12324848	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1288861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1288863	1.00[CHB][hapmap]
rs1288865	1.00[CHB][hapmap]
rs16940351	0.91[JPT][hapmap]
rs16941238	1.00[JPT][hapmap];0.85[TSI][hapmap]
rs16943025	0.92[LWK][hapmap]
rs16943078	0.92[LWK][hapmap]
rs16944629	0.88[CHB][hapmap]
rs1706799	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17533116	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17533716	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17535381	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17537244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17618294	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2088164	0.88[CHB][hapmap]
rs2433229	0.83[JPT][hapmap]
rs2433600	0.88[CHB][hapmap]
rs2433602	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2453546	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2461706	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2486287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2668746	0.92[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4448883	0.88[CHB][hapmap]
rs55721266	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55904415	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56267974	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56273246	0.87[ASN][1000 genomes]
rs56306977	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56327050	0.87[ASN][1000 genomes]
rs56937414	0.85[ASN][1000 genomes]
rs56967490	0.87[ASN][1000 genomes]
rs57369693	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57419781	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61301536	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493157	0.88[CHB][hapmap]
rs72709081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709088	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72709089	0.80[AMR][1000 genomes]
rs72709092	0.88[AMR][1000 genomes]
rs72711253	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72711255	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72711259	0.87[ASN][1000 genomes]
rs8023437	0.88[CHB][hapmap]
rs9972405	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9972498	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9972528	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16942066	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45626000-45652000	Weak transcription	Brain Substantia Nigra	brain
2	chr15:45629800-45642000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:45634600-45651600	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:45635200-45641400	Enhancers	HepG2	liver
5	chr15:45635600-45639400	Enhancers	Fetal Intestine Large	intestine
6	chr15:45635600-45641400	Enhancers	Fetal Intestine Small	intestine
7	chr15:45636400-45638400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr15:45636600-45640800	Enhancers	Liver	Liver
9	chr15:45637200-45638600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:45637200-45640200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr15:45638000-45638800	Enhancers	Duodenum Mucosa	Duodenum
12	chr15:45638000-45639400	Enhancers	Stomach Mucosa	stomach
13	chr15:45638000-45639600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:45638000-45639600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:45638200-45638400	Enhancers	Placenta	Placenta
16	chr15:45638200-45638600	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr15:45638200-45638800	Enhancers	Fetal Lung	lung
18	chr15:45638200-45638800	Enhancers	Small Intestine	intestine
19	chr15:45638200-45639200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:45638200-45639400	Enhancers	Pancreas	Pancrea

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