Variant report

Variant	rs12050725
Chromosome Location	chr15:83590345-83590346
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	GATA3	chr15:83589989-83590496	MCF-7	breast:	n/a	chr15:83590102-83590109 chr15:83590102-83590109 chr15:83590102-83590109 chr15:83590098-83590114
2	ZNF263	chr15:83590033-83590422	HEK293-T-REx	kidney:	n/a	chr15:83590134-83590143
3	GATA3	chr15:83589940-83590465	MCF-7	breast:	n/a	chr15:83590102-83590109 chr15:83590102-83590109 chr15:83590102-83590109 chr15:83590098-83590114
4	SIN3AK20	chr15:83589728-83590559	MCF-7	breast:	n/a	n/a
5	MAX	chr15:83589877-83590394	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:83587802..83590481-chr15:83594024..83596342,2	K562	blood:
2	chr15:83586563..83590594-chr15:83604214..83607566,4	MCF-7	breast:
3	chr15:83571600..83574861-chr15:83589343..83591818,3	K562	blood:
4	chr15:83584751..83586283-chr15:83589059..83590838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259805	TF binding region
ENSG00000259805	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1037403	0.95[JPT][hapmap]
rs11259960	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12148275	1.00[JPT][hapmap]
rs12441675	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1568657	0.89[JPT][hapmap]
rs2046070	0.94[JPT][hapmap]
rs2061947	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2123157	0.94[JPT][hapmap]
rs2167602	0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs4842917	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4842928	0.84[AMR][1000 genomes]
rs4842935	0.94[JPT][hapmap]
rs4843141	1.00[JPT][hapmap]
rs4843144	0.80[JPT][hapmap]
rs4843146	0.93[JPT][hapmap]
rs6603041	0.94[JPT][hapmap]
rs8025253	0.81[AMR][1000 genomes]
rs8043020	0.94[JPT][hapmap]
rs872598	0.81[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs872599	0.94[JPT][hapmap]

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
rs12050725	HOMER2	cis	Nerve Tibial	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83570400-83591600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:83582600-83592600	Enhancers	Liver	Liver
3	chr15:83583200-83597200	Enhancers	Pancreas	Pancrea
4	chr15:83585600-83599200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:83585800-83600000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:83586600-83619400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:83587600-83590400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:83587600-83591000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr15:83587600-83591000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr15:83587600-83594000	Weak transcription	Spleen	Spleen
11	chr15:83588200-83590400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:83588200-83596600	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:83588600-83591000	Weak transcription	Brain Angular Gyrus	brain
14	chr15:83588800-83611600	Weak transcription	Right Atrium	heart
15	chr15:83589400-83590400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:83589400-83602800	Weak transcription	Esophagus	oesophagus
17	chr15:83589600-83591000	Weak transcription	HepG2	liver
18	chr15:83589600-83605400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:83590000-83590400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:83590000-83590400	Enhancers	Ovary	ovary
21	chr15:83590000-83590800	Enhancers	Right Ventricle	heart
22	chr15:83590000-83591800	Enhancers	Left Ventricle	heart
23	chr15:83590000-83592000	Enhancers	Fetal Muscle Leg	muscle
24	chr15:83590000-83594200	Enhancers	Gastric	stomach
25	chr15:83590200-83590400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:83590200-83590400	Bivalent Enhancer	K562	blood
27	chr15:83590200-83591800	Enhancers	Fetal Heart	heart
28	chr15:83590200-83592000	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links