Variant report

Variant	rs56178382
Chromosome Location	chr15:75898996-75898997
allele	A/T
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	chr15:75898585-75900108	PBDE	blood:	n/a	n/a
2	TEAD4	chr15:75898995-75899488	K562	blood:	n/a	n/a
3	GATA1	chr15:75898769-75900540	PBDE	blood:	n/a	chr15:75899260-75899281 chr15:75899265-75899275 chr15:75899265-75899274 chr15:75900332-75900339 chr15:75899267-75899274 chr15:75899877-75899885
4	RUNX3	chr15:75898925-75899604	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75898763..75900517-chr15:75928624..75930263,2	K562	blood:
2	chr15:75897776..75901104-chr15:75901973..75906290,3	MCF-7	breast:

Variant related genes	Relation type
SNUPN	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1128585	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28372916	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28372917	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3210683	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886453	0.86[EUR][1000 genomes]
rs4886723	0.91[EUR][1000 genomes]
rs55737327	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267307	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436854	0.84[EUR][1000 genomes]
rs8025681	0.88[EUR][1000 genomes]
rs8027749	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8041160	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	nsv482802	chr15:75686519-75899896	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
8	nsv531902	chr15:75724505-75919237	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
10	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs56178382	CTD-2323K18.1	cis	Thyroid	GTEx
rs56178382	SNUPN	cis	Thyroid	GTEx
rs56178382	MAN2C1	cis	Esophagus Muscularis	GTEx
rs56178382	CTD-2323K18.1	cis	lung	GTEx
rs56178382	MAN2C1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75876800-75899200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:75877600-75901800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:75880400-75912400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:75882200-75910400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:75882800-75911400	Strong transcription	Fetal Muscle Leg	muscle
6	chr15:75883400-75911800	Strong transcription	Fetal Stomach	stomach
7	chr15:75883600-75901000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr15:75883800-75903600	Strong transcription	Stomach Smooth Muscle	stomach
9	chr15:75883800-75911600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:75883800-75911800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr15:75886000-75912400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:75886200-75903200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr15:75886400-75905400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:75886600-75903400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:75887600-75912400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:75889400-75917600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr15:75889800-75912600	Weak transcription	Right Atrium	heart
18	chr15:75889800-75917600	Weak transcription	Fetal Heart	heart
19	chr15:75890600-75899600	Weak transcription	Fetal Kidney	kidney
20	chr15:75890600-75903200	Strong transcription	Adipose Nuclei	Adipose
21	chr15:75890600-75917000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:75891000-75899200	Weak transcription	Fetal Brain Male	brain
23	chr15:75891000-75917200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:75891800-75912400	Weak transcription	Stomach Mucosa	stomach
25	chr15:75892000-75903600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:75892000-75913200	Strong transcription	Liver	Liver
27	chr15:75892600-75903200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:75892800-75899000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:75892800-75899000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:75893200-75901800	Weak transcription	HMEC	breast
31	chr15:75894800-75903200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:75894800-75910000	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr15:75894800-75913400	Strong transcription	Fetal Intestine Large	intestine
34	chr15:75895000-75903600	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:75895200-75903200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:75895600-75899000	Strong transcription	Osteobl	bone
37	chr15:75895800-75903200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:75896000-75899000	Strong transcription	HSMM	muscle
39	chr15:75896000-75900200	Strong transcription	Hela-S3	cervix
40	chr15:75896000-75902600	Strong transcription	Primary B cells from cord blood	blood
41	chr15:75896000-75903000	Strong transcription	Brain Anterior Caudate	brain
42	chr15:75896000-75903000	Strong transcription	Rectal Smooth Muscle	rectum
43	chr15:75896000-75903200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:75896000-75903200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:75896000-75903200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:75896000-75903200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:75896000-75903200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:75896000-75903200	Strong transcription	NHEK	skin
49	chr15:75896000-75911800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr15:75896000-75912400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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