Variant report

Variant	rs12612789
Chromosome Location	chr2:95527678-95527679
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	ELF1	chr2:95527274-95527966	GM12878	blood:	n/a	n/a
2	SUZ12	chr2:95526764-95528313	NT2-D1	testis:	n/a	n/a
3	HMGN3	chr2:95527408-95527776	K562	blood:	n/a	n/a

Variant related genes	Relation type
ANKRD20A8P	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10165220	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10180591	0.84[ASN][1000 genomes]
rs10874467	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11164111	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11883879	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13414018	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2004626	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2077443	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28680439	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34087291	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4854231	0.92[EUR][1000 genomes]
rs4854232	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4854233	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4854234	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62146933	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62146942	0.82[ASN][1000 genomes]
rs6736042	0.82[AFR][1000 genomes]
rs749308	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2759075	chr2:95358799-95620108	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12612789	AC073464.7	cis	Esophagus Mucosa	GTEx
rs12612789	CYP4F32P	cis	Esophagus Mucosa	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95523800-95527800	Weak transcription	Gastric	stomach
2	chr2:95527000-95527800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr2:95527000-95527800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr2:95527000-95527800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr2:95527000-95527800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:95527000-95527800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
7	chr2:95527000-95528000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr2:95527000-95528000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr2:95527000-95528000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr2:95527200-95527800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:95527200-95527800	Bivalent Enhancer	Adipose Nuclei	Adipose
12	chr2:95527200-95528000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:95527200-95528000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:95527200-95528000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:95527200-95528000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:95527200-95528000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:95527200-95528000	Bivalent Enhancer	Fetal Brain Female	brain
18	chr2:95527200-95528000	ZNF genes & repeats	Spleen	Spleen
19	chr2:95527200-95528200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:95527200-95528200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:95527200-95528200	Enhancers	Pancreas	Pancrea
22	chr2:95527200-95528400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:95527400-95527800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:95527400-95527800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:95527400-95527800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
26	chr2:95527400-95527800	Bivalent Enhancer	Brain Germinal Matrix	brain
27	chr2:95527400-95527800	Bivalent Enhancer	Placenta	Placenta
28	chr2:95527400-95527800	Enhancers	Lung	lung
29	chr2:95527400-95528000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
30	chr2:95527400-95528000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr2:95527400-95528000	Bivalent Enhancer	Fetal Stomach	stomach
32	chr2:95527400-95528200	Bivalent Enhancer	Right Ventricle	heart
33	chr2:95527600-95527800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
34	chr2:95527600-95527800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:95527600-95527800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:95527600-95527800	Bivalent Enhancer	HMEC	breast
37	chr2:95527600-95528000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr2:95527600-95528000	ZNF genes & repeats	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links