Variant report

Variant	rs13158948
Chromosome Location	chr5:147699700-147699701
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	GATA2	chr5:147699698-147700048	SH-SY5Y	brain:	n/a	n/a
2	YY1	chr5:147699381-147699712	SK-N-SH_RA	brain:	n/a	n/a
3	YY1	chr5:147699378-147700012	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr5:147699669-147699768	MCF-7	breast:	n/a	n/a
5	POLR2A	chr5:147699519-147700276	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3A	chr5:147699698-147699909	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:147699674-147699740	MCF-7	breast:	n/a	n/a
8	TAF1	chr5:147699454-147700100	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr5:147699692-147700087	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:147699395-147700082	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr5:147699530-147700087	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SPINK9	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10036053	0.85[EUR][1000 genomes]
rs10037318	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10044054	0.85[EUR][1000 genomes]
rs10050560	0.85[EUR][1000 genomes]
rs10057472	0.81[EUR][1000 genomes]
rs10068891	0.89[EUR][1000 genomes]
rs10072817	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10072958	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10476892	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10477374	0.85[EUR][1000 genomes]
rs10515610	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12516267	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12519039	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12521065	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12717971	0.82[EUR][1000 genomes]
rs13153619	0.86[EUR][1000 genomes]
rs13157347	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13176114	0.89[EUR][1000 genomes]
rs13358385	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1363704	0.85[EUR][1000 genomes]
rs1363705	0.80[EUR][1000 genomes]
rs1363707	0.81[EUR][1000 genomes]
rs1422968	0.82[EUR][1000 genomes]
rs1422970	0.82[EUR][1000 genomes]
rs1582519	0.88[EUR][1000 genomes]
rs17719578	0.89[EUR][1000 genomes]
rs17719662	0.85[EUR][1000 genomes]
rs17719763	0.84[EUR][1000 genomes]
rs17719873	0.82[EUR][1000 genomes]
rs17776554	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17776674	0.81[EUR][1000 genomes]
rs1862430	0.89[EUR][1000 genomes]
rs1862431	0.85[EUR][1000 genomes]
rs2161432	0.86[EUR][1000 genomes]
rs2216653	0.86[EUR][1000 genomes]
rs2400509	0.89[EUR][1000 genomes]
rs2400510	0.89[EUR][1000 genomes]
rs28442279	0.81[EUR][1000 genomes]
rs2895761	0.82[EUR][1000 genomes]
rs34001290	0.88[EUR][1000 genomes]
rs34163281	0.89[EUR][1000 genomes]
rs35006442	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35700061	0.82[EUR][1000 genomes]
rs35792476	0.89[EUR][1000 genomes]
rs3749689	0.85[EUR][1000 genomes]
rs3749690	0.89[EUR][1000 genomes]
rs4705248	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705249	0.85[EUR][1000 genomes]
rs4705251	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4705252	0.88[EUR][1000 genomes]
rs6580542	0.89[EUR][1000 genomes]
rs6580544	0.84[EUR][1000 genomes]
rs6580545	0.84[EUR][1000 genomes]
rs6580546	0.84[EUR][1000 genomes]
rs6580548	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6860261	0.83[EUR][1000 genomes]
rs6865036	0.87[EUR][1000 genomes]
rs6865972	0.88[EUR][1000 genomes]
rs6866106	0.85[EUR][1000 genomes]
rs6875252	0.89[EUR][1000 genomes]
rs6875795	0.81[EUR][1000 genomes]
rs6876308	0.81[EUR][1000 genomes]
rs6876982	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6882932	0.88[EUR][1000 genomes]
rs6886203	0.85[EUR][1000 genomes]
rs6891724	0.85[EUR][1000 genomes]
rs6892647	0.84[EUR][1000 genomes]
rs6893378	0.88[EUR][1000 genomes]
rs6894032	0.86[EUR][1000 genomes]
rs7712350	0.81[EUR][1000 genomes]
rs7713986	0.89[EUR][1000 genomes]
rs7716578	0.85[EUR][1000 genomes]
rs7722458	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7729309	0.88[EUR][1000 genomes]
rs7730707	0.84[EUR][1000 genomes]
rs7731526	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7734458	0.89[EUR][1000 genomes]
rs7736728	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9325094	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9784645	0.86[EUR][1000 genomes]
rs999741	0.86[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	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv599945	chr5:147649181-147720487	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1801220	chr5:147694648-147705789	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147698600-147700400	Active TSS	Fetal Lung	lung
2	chr5:147699400-147700600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr5:147699400-147700600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr5:147699400-147700600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr5:147699400-147700600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr5:147699400-147700600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:147699400-147700600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:147699400-147700600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:147699400-147700600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
10	chr5:147699400-147700600	Active TSS	Fetal Intestine Small	intestine
11	chr5:147699600-147699800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:147699600-147699800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:147699600-147700000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr5:147699600-147700000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:147699600-147700000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:147699600-147700000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:147699600-147700000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:147699600-147700000	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr5:147699600-147700000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:147699600-147700000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:147699600-147700000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:147699600-147700000	Active TSS	Brain Germinal Matrix	brain
23	chr5:147699600-147700000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:147699600-147700000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr5:147699600-147700000	Active TSS	Fetal Brain Female	brain
26	chr5:147699600-147700000	Active TSS	Fetal Kidney	kidney
27	chr5:147699600-147700000	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr5:147699600-147700000	Active TSS	Fetal Muscle Leg	muscle
29	chr5:147699600-147700000	Active TSS	Gastric	stomach
30	chr5:147699600-147700000	Active TSS	Left Ventricle	heart
31	chr5:147699600-147700000	Active TSS	Lung	lung
32	chr5:147699600-147700000	Active TSS	Placenta Amnion	Placenta Amnion
33	chr5:147699600-147700000	Active TSS	A549	lung
34	chr5:147699600-147700000	Active TSS	NHEK	skin
35	chr5:147699600-147700400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:147699600-147700400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:147699600-147700400	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr5:147699600-147700400	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr5:147699600-147700400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:147699600-147700400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:147699600-147700400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr5:147699600-147700400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr5:147699600-147700400	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr5:147699600-147700400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:147699600-147700400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:147699600-147700400	Active TSS	Duodenum Mucosa	Duodenum
47	chr5:147699600-147700400	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr5:147699600-147700400	Active TSS	Fetal Stomach	stomach
49	chr5:147699600-147700400	Active TSS	Ovary	ovary
50	chr5:147699600-147700400	Active TSS	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links