Variant report

Variant	rs2446304
Chromosome Location	chr4:89825872-89825873
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1246629	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246631	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246632	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246634	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1246642	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13110699	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1379932	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1379933	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1458551	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1563689	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2125409	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2446300	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2446301	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2446303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464522	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2464523	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2464528	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609255	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609258	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2609259	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2609260	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2609261	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2609262	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2609264	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609279	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2609280	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2704570	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2704581	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704582	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704583	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704587	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704604	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869952	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904255	0.87[ASN][1000 genomes]
rs4505789	0.85[ASN][1000 genomes]
rs4693974	0.81[ASN][1000 genomes]
rs6813090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815970	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7673818	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7690839	0.84[ASN][1000 genomes]
rs9997652	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv879532	chr4:89811195-89917135	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89809200-89828800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:89816000-89829000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:89816600-89827400	Weak transcription	Fetal Kidney	kidney
4	chr4:89816800-89827800	Weak transcription	Fetal Brain Male	brain
5	chr4:89818000-89829000	Weak transcription	Pancreas	Pancrea
6	chr4:89818800-89828800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:89820000-89859200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:89821400-89826000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:89821600-89827800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:89821800-89829200	Weak transcription	Osteobl	bone
11	chr4:89822800-89828400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:89824200-89826600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:89824400-89829000	Weak transcription	Fetal Intestine Large	intestine
14	chr4:89824600-89834000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:89824800-89829000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:89825000-89826400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr4:89825000-89828600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr4:89825000-89831200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:89825200-89826000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:89825200-89826400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:89825200-89829000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:89825400-89826000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr4:89825400-89826600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:89825600-89826000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:89825600-89826000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:89825600-89826000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr4:89825600-89826800	Strong transcription	Fetal Stomach	stomach
28	chr4:89825600-89827000	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:89825600-89827200	Strong transcription	Placenta	Placenta
30	chr4:89825600-89827400	Strong transcription	Ovary	ovary
31	chr4:89825600-89827600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:89825600-89878400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:89825800-89826000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:89825800-89826000	ZNF genes & repeats	Adipose Nuclei	Adipose
35	chr4:89825800-89826000	ZNF genes & repeats	Fetal Muscle Leg	muscle
36	chr4:89825800-89826600	Strong transcription	Fetal Intestine Small	intestine
37	chr4:89825800-89827000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:89825800-89827200	Strong transcription	Fetal Lung	lung
39	chr4:89825800-89828800	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links