Variant report

Variant	rs13236456
Chromosome Location	chr7:99675558-99675559
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	chr7:99675326-99675610	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99611430..99615857-chr7:99675156..99681193,15	K562	blood:
2	chr7:99668310..99676246-chr7:99677185..99681836,16	MCF-7	breast:

Variant related genes	Relation type
ZNF3	TF binding region
ENSG00000106261	Chromatin interaction
ENSG00000166526	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1141057	0.80[EUR][1000 genomes]
rs35058708	0.80[EUR][1000 genomes]
rs4729567	0.80[EUR][1000 genomes]
rs4729572	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6960432	0.84[AFR][1000 genomes];0.81[EUR][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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers 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	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13236456	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs13236456	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs13236456	AP4M1	cis	Artery Tibial	GTEx
rs13236456	AP4M1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99666400-99677200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:99666400-99678000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:99666800-99677000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:99669600-99677600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:99670200-99676600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr7:99670400-99676200	Strong transcription	Brain Hippocampus Middle	brain
7	chr7:99670400-99676400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr7:99670400-99676600	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr7:99670400-99677000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr7:99670600-99675600	Strong transcription	Left Ventricle	heart
11	chr7:99670600-99676000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:99670600-99677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:99670600-99677600	Strong transcription	Primary T cells from cord blood	blood
14	chr7:99670800-99675800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:99670800-99676400	Strong transcription	Dnd41	blood
16	chr7:99670800-99677000	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr7:99670800-99677400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:99670800-99677400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:99671000-99676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:99671000-99676600	Weak transcription	Right Atrium	heart
21	chr7:99671000-99676800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:99671000-99676800	Strong transcription	Fetal Brain Female	brain
23	chr7:99671000-99676800	Weak transcription	Psoas Muscle	Psoas
24	chr7:99671000-99677000	Strong transcription	Placenta	Placenta
25	chr7:99671000-99677000	Strong transcription	NHEK	skin
26	chr7:99671000-99677200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:99671000-99677200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:99671000-99677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:99671400-99676800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:99671400-99677400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr7:99671400-99677400	Strong transcription	HUVEC	blood vessel
32	chr7:99671600-99677400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr7:99671800-99677000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr7:99671800-99677200	Strong transcription	NH-A	brain
35	chr7:99672000-99676600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:99672000-99676600	Strong transcription	Brain Germinal Matrix	brain
37	chr7:99672000-99677000	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:99672000-99677000	Strong transcription	Fetal Thymus	thymus
39	chr7:99672000-99677200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:99672400-99677000	Weak transcription	Small Intestine	intestine
41	chr7:99673000-99676400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:99673000-99676600	Strong transcription	Fetal Lung	lung
43	chr7:99673000-99677600	Strong transcription	Osteobl	bone
44	chr7:99673000-99677800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr7:99673200-99676800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:99673400-99676800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:99673400-99677400	Weak transcription	NHDF-Ad	bronchial
48	chr7:99673400-99677600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr7:99673400-99677600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr7:99673400-99677800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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