Variant report

Variant	rs10152697
Chromosome Location	chr15:45689929-45689930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr15:45689430-45689942	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SPATA5L1	TF binding region
GATM	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10152337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851425	1.00[CHB][hapmap]
rs1153830	0.86[CHB][hapmap]
rs1153831	0.86[CHB][hapmap]
rs1153832	0.86[CHB][hapmap]
rs12324848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1288861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1288863	1.00[CHB][hapmap]
rs1288865	1.00[CHB][hapmap]
rs16941238	1.00[JPT][hapmap]
rs16942066	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16943025	1.00[YRI][hapmap]
rs16943078	1.00[YRI][hapmap]
rs16944629	0.86[CHB][hapmap]
rs16952731	0.86[CHB][hapmap]
rs1706799	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17533116	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17533716	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17535381	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17537244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17618294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088164	0.86[CHB][hapmap]
rs2433600	0.86[CHB][hapmap]
rs2433602	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453546	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2461706	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2486287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668746	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4448883	0.86[CHB][hapmap]
rs55721266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55904415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267974	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56273246	0.96[ASN][1000 genomes]
rs56306977	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56327050	0.96[ASN][1000 genomes]
rs56937414	0.93[ASN][1000 genomes]
rs56967490	0.96[ASN][1000 genomes]
rs57369693	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57419781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61301536	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493157	0.86[CHB][hapmap]
rs6493158	0.86[CHB][hapmap]
rs7165838	0.85[CHB][hapmap]
rs7173983	0.86[CHB][hapmap]
rs72709081	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72709084	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72709088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709089	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72709092	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72711253	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711255	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711259	0.96[ASN][1000 genomes]
rs8023437	0.86[CHB][hapmap]
rs8042811	0.86[CHB][hapmap]
rs9972405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972528	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs10152697	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45679000-45693800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:45682800-45693800	Weak transcription	Brain Angular Gyrus	brain
3	chr15:45683200-45691600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:45685600-45691800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr15:45685600-45692800	Weak transcription	GM12878-XiMat	blood
6	chr15:45686800-45693600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:45687200-45691600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:45687200-45693800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:45687400-45693200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:45688200-45691600	Weak transcription	Brain Anterior Caudate	brain
11	chr15:45688200-45691600	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:45688400-45691400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:45688400-45691600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:45688400-45693400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:45688800-45690200	Enhancers	Pancreas	Pancrea
16	chr15:45688800-45690800	Weak transcription	Liver	Liver
17	chr15:45688800-45693600	Weak transcription	Brain Substantia Nigra	brain
18	chr15:45689600-45690200	Enhancers	Fetal Intestine Large	intestine
19	chr15:45689800-45690000	Enhancers	Duodenum Mucosa	Duodenum
20	chr15:45689800-45690000	Enhancers	Small Intestine	intestine
21	chr15:45689800-45690200	Enhancers	Fetal Intestine Small	intestine
22	chr15:45689800-45690200	Enhancers	HepG2	liver
23	chr15:45689800-45693200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:45689800-45693200	Weak transcription	Rectal Mucosa Donor 31	rectum

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