Variant report

Variant	rs4240204
Chromosome Location	chr2:86840286-86840287
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86835703..86840288-chr2:86849045..86852992,6	K562	blood:
2	chr2:86788949..86791778-chr2:86837790..86840481,3	MCF-7	breast:
3	chr2:86839004..86842325-chr2:86847581..86852030,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239305	Chromatin interaction
ENSG00000115561	Chromatin interaction
ENSG00000228363	Chromatin interaction
ENSG00000249884	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10187753	0.81[EUR][1000 genomes]
rs12623509	0.81[EUR][1000 genomes]
rs4832043	0.81[EUR][1000 genomes]
rs4832303	0.81[EUR][1000 genomes]
rs6733569	0.81[EUR][1000 genomes]
rs737463	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4240204	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86823200-86842800	Weak transcription	Psoas Muscle	Psoas
2	chr2:86824600-86840600	Weak transcription	Fetal Heart	heart
3	chr2:86825400-86849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:86826800-86842000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:86826800-86847800	Weak transcription	NHEK	skin
6	chr2:86828200-86847800	Weak transcription	NHLF	lung
7	chr2:86829000-86845400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:86829400-86848400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:86829400-86849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:86829600-86846200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:86829800-86846000	Weak transcription	NH-A	brain
12	chr2:86829800-86849400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:86830000-86846200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:86830000-86848600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:86830400-86846200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:86830400-86847600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:86830400-86848600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:86830600-86847000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:86830800-86845000	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:86830800-86845600	Strong transcription	Dnd41	blood
21	chr2:86830800-86847600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:86830800-86847800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:86830800-86848000	Strong transcription	Placenta	Placenta
24	chr2:86831000-86842600	Strong transcription	Liver	Liver
25	chr2:86831000-86842800	Strong transcription	Fetal Intestine Large	intestine
26	chr2:86831000-86847200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:86831800-86843200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:86831800-86848000	Weak transcription	HMEC	breast
29	chr2:86831800-86848200	Weak transcription	K562	blood
30	chr2:86832000-86840800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:86832200-86848200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:86832400-86840800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:86832400-86849400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:86832600-86841000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:86832600-86844600	Weak transcription	Fetal Brain Male	brain
36	chr2:86832600-86844600	Weak transcription	Small Intestine	intestine
37	chr2:86832600-86848200	Weak transcription	Colonic Mucosa	Colon
38	chr2:86833000-86848200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:86834000-86846800	Strong transcription	Fetal Lung	lung
40	chr2:86834400-86842800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:86834400-86846600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:86834400-86847000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:86834600-86844600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr2:86834600-86847400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:86834600-86847800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr2:86835200-86843000	Strong transcription	A549	lung
47	chr2:86835200-86843200	Strong transcription	Brain Anterior Caudate	brain
48	chr2:86835200-86847200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr2:86835200-86847800	Weak transcription	Hela-S3	cervix
50	chr2:86835400-86845200	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links