Variant report

Variant	rs3790015
Chromosome Location	chr13:51640421-51640422
allele	A/G
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	CTCF	chr13:51640280-51640430	GM06990	blood:	n/a	n/a
2	CTCF	chr13:51640300-51640450	GM12874	blood:	n/a	n/a
3	CTCF	chr13:51640207-51640421	K562	blood:	n/a	n/a
4	RAD21	chr13:51640053-51640527	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr13:51640164-51640464	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr13:51640280-51640430	GM12864	blood:	n/a	n/a
7	CTCF	chr13:51640280-51640430	GM12871	blood:	n/a	n/a
8	CTCF	chr13:51640280-51640430	GM12868	blood:	n/a	n/a
9	CTCF	chr13:51640300-51640450	GM06990	blood:	n/a	n/a
10	CTCF	chr13:51640300-51640450	GM12870	blood:	n/a	n/a
11	CTCF	chr13:51640300-51640450	GM12867	blood:	n/a	n/a
12	CTCF	chr13:51640300-51640450	GM12865	blood:	n/a	n/a

Variant related genes	Relation type
GUCY1B2	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11148205	0.88[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11842080	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12859216	0.88[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12865698	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12871332	0.94[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12877403	0.89[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs3790017	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803198	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs3803199	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3803200	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4606607	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71428302	0.84[EUR][1000 genomes]
rs913467	0.82[CHB][hapmap]
rs927992	0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9526717	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9563015	0.94[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9563017	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9563018	0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9563019	0.86[EUR][1000 genomes]
rs9563020	0.85[EUR][1000 genomes]
rs9568502	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568503	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568504	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568505	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832610	chr13:51636661-51822106	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51633200-51641000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr13:51633400-51657800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:51633800-51640800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:51634400-51640800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:51637000-51641600	Enhancers	Primary hematopoietic stem cells	blood
6	chr13:51638000-51640800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:51638000-51644600	Enhancers	Fetal Brain Male	brain
8	chr13:51638400-51640600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:51638800-51640800	Enhancers	Fetal Brain Female	brain
10	chr13:51638800-51641000	Enhancers	Fetal Lung	lung
11	chr13:51639200-51641200	Enhancers	Spleen	Spleen
12	chr13:51639200-51644000	Weak transcription	Fetal Kidney	kidney
13	chr13:51639400-51641400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr13:51639400-51641600	Enhancers	Fetal Muscle Leg	muscle
15	chr13:51639600-51640800	Bivalent Enhancer	HMEC	breast
16	chr13:51639600-51641000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:51639600-51641400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr13:51639600-51641400	Bivalent Enhancer	HUVEC	blood vessel
19	chr13:51639600-51641600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr13:51639600-51641600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr13:51639800-51640600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr13:51639800-51641000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:51639800-51641000	Bivalent Enhancer	GM12878-XiMat	blood
24	chr13:51639800-51641600	Enhancers	Fetal Stomach	stomach
25	chr13:51639800-51642200	Weak transcription	HepG2	liver
26	chr13:51640000-51641000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr13:51640000-51641000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr13:51640000-51641000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:51640000-51641200	Enhancers	Lung	lung
30	chr13:51640000-51641600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr13:51640000-51641800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr13:51640000-51644200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr13:51640200-51640600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr13:51640200-51640600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:51640200-51641000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr13:51640200-51641000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr13:51640200-51641400	Enhancers	Adipose Nuclei	Adipose
38	chr13:51640200-51644600	Enhancers	Fetal Heart	heart
39	chr13:51640400-51640800	Enhancers	Brain Angular Gyrus	brain
40	chr13:51640400-51641000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:51640400-51641000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
42	chr13:51640400-51641000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
43	chr13:51640400-51641000	Enhancers	Gastric	stomach
44	chr13:51640400-51641000	Enhancers	NH-A	brain
45	chr13:51640400-51641000	Bivalent Enhancer	Osteobl	bone
46	chr13:51640400-51641200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr13:51640400-51641200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr13:51640400-51641200	Enhancers	Right Atrium	heart
49	chr13:51640400-51641200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr13:51640400-51641400	Flanking Active TSS	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links