Variant report

Variant	rs28451607
Chromosome Location	chr15:83655726-83655727
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr15:83653932-83655807	MCF-7	breast:	n/a	chr15:83654951-83654958

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:83620048..83621695-chr15:83654415..83656923,3	MCF-7	breast:
2	chr15:83653840..83656336-chr16:14164975..14167418,2	MCF-7	breast:
3	chr15:83417301..83420117-chr15:83653856..83657124,3	MCF-7	breast:
4	chr15:83517113..83521654-chr15:83652714..83657006,7	MCF-7	breast:
5	chr15:83655503..83657739-chr15:83659649..83661326,2	K562	blood:
6	chr15:83652926..83655970-chr15:83874776..83878125,3	MCF-7	breast:
7	chr15:83654223..83656996-chr15:83678905..83681492,4	MCF-7	breast:

No data

Variant related genes	Relation type
HOMER2	TF binding region
ENSG00000103942	Chromatin interaction
ENSG00000169609	Chromatin interaction
ENSG00000250988	Chromatin interaction
ENSG00000260608	Chromatin interaction
ENSG00000186260	Chromatin interaction
ENSG00000166503	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1037403	0.95[ASN][1000 genomes]
rs11259963	0.94[ASN][1000 genomes]
rs2046070	0.97[ASN][1000 genomes]
rs2123157	0.95[ASN][1000 genomes]
rs2123158	0.95[ASN][1000 genomes]
rs2167602	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2381028	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28510273	0.88[ASN][1000 genomes]
rs4842859	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4842928	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4842935	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59108707	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6603038	0.97[ASN][1000 genomes]
rs6603041	0.89[ASN][1000 genomes]
rs8025253	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034220	0.82[ASN][1000 genomes]
rs8043020	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28451607	HOMER2	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83654000-83656000	Active TSS	Colonic Mucosa	Colon
2	chr15:83654000-83656400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:83654200-83655800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr15:83654200-83655800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:83654200-83655800	Active TSS	Aorta	Aorta
6	chr15:83654200-83656000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:83654200-83656000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:83654200-83656000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:83654200-83656000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:83654200-83656200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:83654400-83655800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:83654400-83655800	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr15:83654400-83655800	Active TSS	Gastric	stomach
14	chr15:83654400-83655800	Active TSS	Ovary	ovary
15	chr15:83654400-83655800	Active TSS	Rectal Smooth Muscle	rectum
16	chr15:83654400-83655800	Active TSS	Small Intestine	intestine
17	chr15:83654400-83656000	Active TSS	Brain Hippocampus Middle	brain
18	chr15:83654400-83656000	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr15:83654400-83656200	Active TSS	Psoas Muscle	Psoas
20	chr15:83654400-83656400	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr15:83654600-83655800	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr15:83654600-83655800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr15:83654600-83655800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:83654600-83655800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:83654600-83655800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:83654600-83655800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr15:83654600-83655800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:83654600-83655800	Active TSS	Brain Angular Gyrus	brain
29	chr15:83654600-83655800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:83654600-83655800	Active TSS	Colon Smooth Muscle	Colon
31	chr15:83654600-83655800	Active TSS	Duodenum Mucosa	Duodenum
32	chr15:83654600-83655800	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr15:83654600-83655800	Active TSS	Fetal Intestine Large	intestine
34	chr15:83654600-83655800	Active TSS	Fetal Intestine Small	intestine
35	chr15:83654600-83655800	Active TSS	Fetal Thymus	thymus
36	chr15:83654600-83655800	Active TSS	Placenta Amnion	Placenta Amnion
37	chr15:83654600-83655800	Active TSS	Right Atrium	heart
38	chr15:83654600-83655800	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr15:83654600-83655800	Active TSS	HSMM	muscle
40	chr15:83654600-83656000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:83654600-83656000	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr15:83654600-83656000	Active TSS	A549	lung
43	chr15:83654600-83656000	Active TSS	NHLF	lung
44	chr15:83654600-83656000	Active TSS	Osteobl	bone
45	chr15:83654600-83656200	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr15:83654600-83656200	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr15:83654600-83656200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:83654600-83656200	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr15:83654600-83656200	Active TSS	Fetal Lung	lung
50	chr15:83654600-83656200	Active TSS	Stomach Smooth Muscle	stomach

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