Variant report

Variant	rs786452
Chromosome Location	chr12:124057169-124057170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:124047707..124050611-chr12:124054919..124057365,3	MCF-7	breast:
2	chr12:124056996..124059825-chr12:124068978..124071238,2	MCF-7	breast:
3	chr12:124041024..124043349-chr12:124054707..124057427,2	MCF-7	breast:
4	chr12:124017387..124020298-chr12:124054468..124057519,3	MCF-7	breast:
5	chr12:124056030..124058750-chr12:124059393..124062222,4	K562	blood:
6	chr1:150334954..150337894-chr12:124054865..124057568,2	MCF-7	breast:
7	chr12:124056886..124060484-chr12:124067247..124069927,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163125	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10846531	0.89[CHB][hapmap]
rs11057307	0.90[ASN][1000 genomes]
rs1515814	0.90[ASN][1000 genomes]
rs2048802	0.89[CHB][hapmap]
rs3748268	0.89[CHB][hapmap]
rs3748269	0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4040225	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4456350	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6488883	0.90[ASN][1000 genomes]
rs6551	0.90[ASN][1000 genomes]
rs7134896	0.90[ASN][1000 genomes]
rs7302183	0.90[ASN][1000 genomes]
rs7313628	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs786422	0.90[ASN][1000 genomes]
rs786423	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs786425	0.90[ASN][1000 genomes]
rs786441	0.88[ASN][1000 genomes]
rs786443	0.90[ASN][1000 genomes]
rs786444	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs786445	0.90[ASN][1000 genomes]
rs786447	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs786448	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs786449	0.90[ASN][1000 genomes]
rs7972413	0.82[ASN][1000 genomes]
rs884892	0.89[CHB][hapmap]

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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS 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	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs786452	PXN	cis	cerebellum	SCAN
rs786452	DDX55	cis	cerebellum	SCAN
rs786452	DDX55	cis	multi-tissue	Pritchard
rs786452	TCTN2	cis	cerebellum	SCAN
rs786452	DDX55	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124055000-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:124055000-124067400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:124055200-124060800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:124055200-124068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:124055400-124067800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:124055800-124060400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:124055800-124060600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:124056000-124060800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:124056000-124066600	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:124056000-124066600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:124056000-124067000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:124056000-124067800	Weak transcription	Lung	lung
13	chr12:124056200-124060600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:124056200-124064800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:124056200-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:124056200-124066600	Weak transcription	Thymus	Thymus
17	chr12:124056200-124067000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:124056200-124067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:124056400-124060400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:124056400-124060400	Weak transcription	A549	lung
21	chr12:124056400-124060600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:124056400-124065200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:124056400-124065400	Weak transcription	Osteobl	bone
24	chr12:124056400-124066600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:124056400-124066600	Weak transcription	Adipose Nuclei	Adipose
26	chr12:124056400-124066600	Weak transcription	Brain Anterior Caudate	brain
27	chr12:124056400-124066600	Weak transcription	K562	blood
28	chr12:124056400-124066800	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:124056400-124066800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:124056400-124067000	Weak transcription	NHDF-Ad	bronchial
31	chr12:124056400-124067400	Weak transcription	HSMMtube	muscle
32	chr12:124056800-124066600	Weak transcription	Dnd41	blood

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