Variant report

Variant	rs4858893
Chromosome Location	chr3:47484797-47484798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1038394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1076394	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs10865946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11130123	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs11130124	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs11130126	0.88[CEU][hapmap]
rs11130128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11130129	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11130137	1.00[CEU][hapmap]
rs11705957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11710013	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs11710121	0.88[CEU][hapmap]
rs11710322	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs11711265	1.00[CEU][hapmap]
rs11711824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11712445	1.00[CEU][hapmap]
rs11716763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11719877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11915074	0.89[CEU][hapmap]
rs11920853	0.89[CEU][hapmap]
rs12490383	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs12495169	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs12636851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13059519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13075233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1531875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1638676	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs17080872	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs17410853	0.88[CEU][hapmap]
rs17411375	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs17784882	1.00[CEU][hapmap]
rs1872164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2101247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2159400	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs2291298	1.00[CEU][hapmap]
rs295428	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs295441	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs295442	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs295449	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs295458	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs295461	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs3736177	1.00[CEU][hapmap]
rs3816779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4683326	0.96[CEU][hapmap]
rs4858811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4858894	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6768221	0.88[CEU][hapmap]
rs6780013	0.92[CEU][hapmap]
rs6792461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6800271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7651762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs807932	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs807936	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs811115	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs878659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs922957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9683033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv511233	chr3:47484797-47494157	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4858893	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs4858893	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47450400-47484800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:47463000-47485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:47463600-47484800	Strong transcription	Primary T cells from cord blood	blood
4	chr3:47471800-47485000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:47472400-47485200	Weak transcription	Fetal Brain Male	brain
6	chr3:47473200-47487200	Weak transcription	HUVEC	blood vessel
7	chr3:47474600-47489600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:47476000-47485800	Weak transcription	Fetal Kidney	kidney
9	chr3:47476600-47485400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:47476600-47514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:47476800-47484800	Weak transcription	NH-A	brain
12	chr3:47478200-47485000	Strong transcription	Dnd41	blood
13	chr3:47478400-47484800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:47479400-47484800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:47479600-47485800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:47480400-47485200	Strong transcription	K562	blood
17	chr3:47480800-47484800	Strong transcription	Thymus	Thymus
18	chr3:47481000-47485000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:47481400-47496000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:47481400-47500600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:47481600-47486000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:47481800-47485000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:47481800-47492600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:47482200-47488800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:47482600-47486400	Enhancers	Stomach Mucosa	stomach
26	chr3:47482800-47485000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:47483000-47486000	Enhancers	Fetal Intestine Large	intestine
28	chr3:47483000-47486400	Enhancers	Fetal Intestine Small	intestine
29	chr3:47483200-47487400	Enhancers	Liver	Liver
30	chr3:47483400-47486000	Enhancers	Pancreas	Pancrea
31	chr3:47483400-47486600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:47483600-47484800	Enhancers	A549	lung
33	chr3:47483600-47485200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:47483600-47485800	Enhancers	Fetal Heart	heart
35	chr3:47483600-47486000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr3:47483800-47485000	Enhancers	Colon Smooth Muscle	Colon
37	chr3:47483800-47485200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:47483800-47485400	Enhancers	Ovary	ovary
39	chr3:47483800-47485600	Enhancers	Esophagus	oesophagus
40	chr3:47483800-47486000	Enhancers	Psoas Muscle	Psoas
41	chr3:47483800-47486000	Enhancers	Right Ventricle	heart
42	chr3:47484000-47485000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:47484000-47485000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:47484000-47485200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:47484000-47486200	Enhancers	Brain Hippocampus Middle	brain
46	chr3:47484000-47507800	Weak transcription	Primary B cells from cord blood	blood
47	chr3:47484000-47511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:47484200-47484800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr3:47484200-47484800	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr3:47484200-47484800	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links