Variant report

Variant	rs4890222
Chromosome Location	chr18:39693417-39693418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10221315	0.90[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs10468957	0.87[ASN][1000 genomes]
rs11082255	0.83[CHB][hapmap]
rs11659568	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11660388	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11660513	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11662171	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12326267	0.87[ASN][1000 genomes]
rs12327365	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12455083	0.83[ASW][hapmap];0.83[CHB][hapmap]
rs12709716	0.82[EUR][1000 genomes]
rs12954202	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12964931	0.87[ASN][1000 genomes]
rs1557418	0.87[ASN][1000 genomes]
rs1557419	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1573497	0.87[ASN][1000 genomes]
rs1941532	0.86[ASN][1000 genomes]
rs2096896	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2096897	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2105680	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3932738	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3932739	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4121811	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890377	0.86[CHB][hapmap]
rs4890379	0.83[CHB][hapmap]
rs514227	0.81[EUR][1000 genomes]
rs536139	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56147258	0.87[ASN][1000 genomes]
rs581950	0.87[CHB][hapmap]
rs584380	0.91[EUR][1000 genomes]
rs62082911	0.88[ASN][1000 genomes]
rs657164	0.83[CHB][hapmap]
rs681048	0.93[EUR][1000 genomes]
rs7237998	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs948871	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs948872	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs948873	0.87[ASN][1000 genomes]
rs9635942	0.87[ASN][1000 genomes]
rs9807114	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1057988	chr18:39618253-39713904	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1065792	chr18:39619676-39711798	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1057790	chr18:39621947-39705550	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	esv2762006	chr18:39621947-39713916	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1063952	chr18:39621947-39718600	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv1064973	chr18:39623604-39711798	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv833631	chr18:39633503-39824091	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1063205	chr18:39678456-39741061	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	nsv1060346	chr18:39678456-39742702	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
14	nsv1067132	chr18:39691269-39808287	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
15	nsv543687	chr18:39691269-39808287	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4890222	PIK3C3	cis	cerebellum	SCAN
rs4890222	PIK3C3	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39691200-39693800	Enhancers	HepG2	liver
2	chr18:39692200-39695600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr18:39692600-39694800	Enhancers	Fetal Intestine Small	intestine
4	chr18:39692800-39694000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr18:39692800-39694800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr18:39693000-39694200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr18:39693000-39695000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr18:39693200-39693800	Enhancers	GM12878-XiMat	blood
9	chr18:39693200-39694000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr18:39693200-39694000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr18:39693200-39694200	Enhancers	Primary hematopoietic stem cells	blood
12	chr18:39693200-39694400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr18:39693200-39694400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr18:39693200-39694800	Enhancers	Dnd41	blood
15	chr18:39693400-39694000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr18:39693400-39694200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr18:39693400-39694200	Enhancers	K562	blood
18	chr18:39693400-39694400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr18:39693400-39694600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr18:39693400-39694600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr18:39693400-39694800	Enhancers	Colon Smooth Muscle	Colon
22	chr18:39693400-39694800	Enhancers	Fetal Intestine Large	intestine
23	chr18:39693400-39694800	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links