Variant report

Variant	rs4858867
Chromosome Location	chr3:47911521-47911522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47908495..47911109-chr3:47911186..47914669,4	K562	blood:
2	chr3:47898431..47902857-chr3:47908612..47913870,6	K562	blood:
3	chr3:47910657..47912296-chr3:48148741..48150868,2	K562	blood:
4	chr3:47911284..47912012-chr3:48192739..48193284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047849	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17079910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17290686	0.91[AMR][1000 genomes]
rs17498376	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs2291903	0.80[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2306794	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3772398	0.98[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4858869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858870	0.98[AMR][1000 genomes]
rs4858883	0.82[AMR][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	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
2	nsv1006560	chr3:47867461-48037031	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv1011662	chr3:47891634-48019462	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv536561	chr3:47891634-48019462	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4858867	KLHL18	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47867800-47918800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:47868000-47915200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47868400-47916400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:47868400-47919000	Strong transcription	Fetal Stomach	stomach
5	chr3:47868600-47912200	Strong transcription	Fetal Intestine Small	intestine
6	chr3:47869000-47918600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:47870800-47931800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:47884600-47918400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:47885000-47914800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:47889800-47912600	Weak transcription	Fetal Heart	heart
11	chr3:47891400-47912000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:47894200-47912200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:47894800-47917400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:47894800-47919400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:47896600-47919600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr3:47896800-47913200	Strong transcription	Fetal Muscle Leg	muscle
17	chr3:47899000-47919000	Weak transcription	Right Atrium	heart
18	chr3:47903800-47915800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:47904000-47915000	Strong transcription	Ovary	ovary
20	chr3:47904000-47915600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:47904000-47918600	Strong transcription	Osteobl	bone
22	chr3:47904200-47913600	Strong transcription	Brain Germinal Matrix	brain
23	chr3:47904200-47915400	Strong transcription	Stomach Smooth Muscle	stomach
24	chr3:47904200-47917400	Strong transcription	HSMM	muscle
25	chr3:47904200-47917400	Strong transcription	NH-A	brain
26	chr3:47904200-47917600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:47904200-47918600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:47904400-47912400	Strong transcription	Fetal Intestine Large	intestine
29	chr3:47904400-47915200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:47904400-47916400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:47904600-47912800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:47904600-47915000	Strong transcription	Colon Smooth Muscle	Colon
33	chr3:47904600-47918600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:47904600-47918800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:47904600-47919000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:47904800-47913000	Strong transcription	Gastric	stomach
37	chr3:47904800-47913600	Strong transcription	Brain Anterior Caudate	brain
38	chr3:47904800-47914800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr3:47904800-47914800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:47904800-47914800	Strong transcription	HMEC	breast
41	chr3:47904800-47915000	Strong transcription	Fetal Brain Female	brain
42	chr3:47904800-47915000	Strong transcription	HepG2	liver
43	chr3:47904800-47915200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:47904800-47915200	Strong transcription	Fetal Thymus	thymus
45	chr3:47904800-47915400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:47904800-47915400	Strong transcription	Primary T cells from cord blood	blood
47	chr3:47904800-47915400	Strong transcription	NHLF	lung
48	chr3:47904800-47916000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:47904800-47916400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:47904800-47916400	Strong transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links