Variant report

Variant	rs1648305
Chromosome Location	chr15:45438537-45438538
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	POLR2A	chr15:45438432-45440451	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45435866..45441707-chr15:45442117..45446619,7	K562	blood:
2	chr15:45428900..45431530-chr15:45437116..45439567,2	K562	blood:

Variant related genes	Relation type
DUOX1	TF binding region
ENSG00000137857	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12438755	0.83[JPT][hapmap]
rs1648306	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1648309	0.88[ASN][1000 genomes]
rs1706778	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706816	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1706818	0.88[ASN][1000 genomes]
rs2292467	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2467821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467825	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55675432	0.97[EUR][1000 genomes]
rs62025132	0.89[EUR][1000 genomes]
rs8043418	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv457124	chr15:45381998-45460422	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv569312	chr15:45381998-45460422	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	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
8	nsv569313	chr15:45413541-45457458	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv457125	chr15:45420718-45450323	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv569314	chr15:45420718-45450323	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv518213	chr15:45421758-45464768	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv520580	chr15:45438537-45457349	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
13	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1648305	C15orf57	cis	parietal	SCAN
rs1648305	SLC30A4	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45426600-45440200	Weak transcription	HMEC	breast
2	chr15:45427600-45458600	Weak transcription	Right Atrium	heart
3	chr15:45428600-45444400	Weak transcription	Pancreas	Pancrea
4	chr15:45428600-45449000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:45429400-45443800	Weak transcription	Ovary	ovary
6	chr15:45430000-45441200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:45430200-45446200	Weak transcription	Brain Anterior Caudate	brain
8	chr15:45431400-45449000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:45431800-45442600	Weak transcription	Fetal Intestine Small	intestine
10	chr15:45434800-45457800	Weak transcription	Adipose Nuclei	Adipose
11	chr15:45435200-45444000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:45436400-45440000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:45436400-45444000	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:45436600-45438800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:45437200-45438800	Weak transcription	Esophagus	oesophagus
16	chr15:45437800-45438800	Weak transcription	Lung	lung
17	chr15:45438200-45438600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:45438200-45438800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:45438200-45438800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:45438200-45438800	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr15:45438200-45439000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:45438200-45439000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:45438200-45439400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:45438200-45439600	Enhancers	Placenta	Placenta
25	chr15:45438400-45439000	Enhancers	Gastric	stomach
26	chr15:45438400-45439000	Enhancers	Stomach Mucosa	stomach
27	chr15:45438400-45439200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr15:45438400-45441600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:45438400-45441600	Genic enhancers	NHEK	skin
30	chr15:45438400-45442600	Weak transcription	Spleen	Spleen

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