Variant report

Variant	rs28429357
Chromosome Location	chr18:7942009-7942010
allele	C/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	TCF12	chr18:7941306-7942095	A549	lung:	n/a	n/a
2	POLR2A	chr18:7941659-7942615	A549	lung:	n/a	n/a
3	GATA3	chr18:7941525-7942097	MCF-7	breast:	n/a	n/a
4	GATA2	chr18:7941537-7942018	SH-SY5Y	brain:	n/a	n/a
5	EP300	chr18:7941439-7942093	A549	lung:	n/a	n/a
6	NR2F2	chr18:7941577-7942033	MCF-7	breast:	n/a	n/a
7	GATA3	chr18:7941484-7942149	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
PTPRM	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10164001	0.92[AFR][1000 genomes]
rs13381990	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28714420	0.92[AFR][1000 genomes]
rs7230073	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7239466	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9954126	0.93[AFR][1000 genomes]
rs9962120	0.80[AFR][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	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv2761987	chr18:7934001-7943335	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7923400-7945800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr18:7926400-7945200	Weak transcription	Ovary	ovary
3	chr18:7926800-7945600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr18:7926800-7945800	Weak transcription	Fetal Lung	lung
5	chr18:7927800-7946600	Weak transcription	Fetal Kidney	kidney
6	chr18:7928000-7946600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr18:7932000-7946000	Weak transcription	Brain Anterior Caudate	brain
8	chr18:7932200-7961000	Weak transcription	HepG2	liver
9	chr18:7933600-7945400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr18:7936800-7944800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr18:7937200-7945800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr18:7937400-7945600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr18:7937600-7945600	Weak transcription	Fetal Stomach	stomach
14	chr18:7937600-7947000	Weak transcription	Thymus	Thymus
15	chr18:7937600-7949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr18:7937600-7955200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr18:7938000-7945600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr18:7938000-7945600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr18:7938000-7946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr18:7939800-7942600	Enhancers	A549	lung
21	chr18:7940200-7942800	Enhancers	Brain Germinal Matrix	brain
22	chr18:7940200-7944200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr18:7940200-7945600	Weak transcription	HSMM	muscle
24	chr18:7940600-7945400	Weak transcription	Aorta	Aorta
25	chr18:7940800-7945000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr18:7940800-7945000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr18:7940800-7945400	Weak transcription	Osteobl	bone
28	chr18:7941000-7942200	Enhancers	Fetal Muscle Leg	muscle
29	chr18:7941000-7942200	Enhancers	Pancreas	Pancrea
30	chr18:7941000-7946600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr18:7941200-7945600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr18:7941200-7945800	Weak transcription	Adipose Nuclei	Adipose
33	chr18:7941400-7942400	Weak transcription	Gastric	stomach
34	chr18:7941400-7955000	Weak transcription	Psoas Muscle	Psoas
35	chr18:7941800-7945000	Weak transcription	Left Ventricle	heart
36	chr18:7941800-7945800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr18:7941800-7945800	Weak transcription	Right Ventricle	heart
38	chr18:7941800-7946000	Weak transcription	Brain Substantia Nigra	brain
39	chr18:7941800-7946800	Weak transcription	Lung	lung
40	chr18:7941800-7966400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr18:7942000-7945400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr18:7942000-7945400	Weak transcription	HMEC	breast
43	chr18:7942000-7945600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr18:7942000-7945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr18:7942000-7945600	Weak transcription	NHEK	skin
46	chr18:7942000-7945800	Weak transcription	Stomach Mucosa	stomach
47	chr18:7942000-7946400	Weak transcription	Right Atrium	heart
48	chr18:7942000-7946600	Weak transcription	Fetal Heart	heart
49	chr18:7942000-7946800	Weak transcription	Brain Angular Gyrus	brain
50	chr18:7942000-7955200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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