Variant report

Variant	rs16941346
Chromosome Location	chr15:59627039-59627040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59625699..59628162-chr15:59663501..59666309,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157483	Chromatin interaction
ENSG00000157470	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12438647	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16941344	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1967039	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1967040	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2414629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28378088	1.00[AMR][1000 genomes]
rs28406496	1.00[AMR][1000 genomes]
rs28775006	0.86[EUR][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv457175	chr15:59609753-59681214	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv569603	chr15:59609753-59681214	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv471246	chr15:59610743-59681214	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1794268	chr15:59614874-59637355	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv904274	chr15:59623576-59689378	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16941346	PDGFD	trans	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59600000-59627400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:59606800-59631600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:59610200-59627200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:59621200-59627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:59622000-59627400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:59622200-59627400	Weak transcription	Fetal Heart	heart
7	chr15:59622600-59631800	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:59623200-59628400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:59623200-59631400	Weak transcription	Right Ventricle	heart
10	chr15:59623200-59662800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:59623400-59630800	Weak transcription	Left Ventricle	heart
12	chr15:59623400-59641200	Weak transcription	Aorta	Aorta
13	chr15:59623400-59643800	Weak transcription	Lung	lung
14	chr15:59623600-59627800	Weak transcription	HSMMtube	muscle
15	chr15:59623600-59636400	Weak transcription	Psoas Muscle	Psoas
16	chr15:59624400-59628200	Enhancers	HepG2	liver
17	chr15:59624400-59637800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:59624600-59627600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:59624600-59650000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:59624800-59627200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:59624800-59627600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:59624800-59631400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:59625000-59627600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:59625000-59636600	Weak transcription	Fetal Intestine Small	intestine
25	chr15:59625200-59627200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:59625400-59627600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:59625400-59628000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:59625400-59628200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr15:59625600-59628600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:59625800-59627400	Enhancers	HMEC	breast
31	chr15:59626000-59627400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:59626000-59632600	Weak transcription	NHLF	lung
33	chr15:59626200-59627200	Weak transcription	Hela-S3	cervix
34	chr15:59626400-59627200	Enhancers	A549	lung
35	chr15:59626400-59627800	Enhancers	NHEK	skin
36	chr15:59626400-59631600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:59626400-59641400	Weak transcription	HUVEC	blood vessel
38	chr15:59626400-59642400	Weak transcription	Pancreas	Pancrea
39	chr15:59626600-59628000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:59626600-59628400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:59626800-59628200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:59626800-59628200	Enhancers	Primary B cells from peripheral blood	blood
43	chr15:59626800-59628200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:59626800-59628200	Enhancers	Brain Angular Gyrus	brain
45	chr15:59626800-59628200	Enhancers	Brain Cingulate Gyrus	brain
46	chr15:59626800-59628200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr15:59626800-59628200	Enhancers	Brain Substantia Nigra	brain
48	chr15:59626800-59628200	Enhancers	NHDF-Ad	bronchial
49	chr15:59626800-59628400	Enhancers	Fetal Brain Male	brain
50	chr15:59626800-59628600	Enhancers	Brain Hippocampus Middle	brain

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