Variant report

Variant	rs7623949
Chromosome Location	chr3:51533039-51533040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:51420258..51423192-chr3:51532829..51535179,2	K562	blood:
2	chr3:51532560..51534895-chr3:51704003..51706915,3	K562	blood:
3	chr3:51532457..51535099-chr3:51703667..51706623,4	MCF-7	breast:
4	chr3:51429853..51431477-chr3:51530962..51533655,2	MCF-7	breast:
5	chr3:51427089..51429647-chr3:51532056..51534012,2	MCF-7	breast:
6	chr3:51426988..51429067-chr3:51532869..51536301,5	K562	blood:
7	chr3:51532744..51536241-chr3:51571123..51575595,5	K562	blood:
8	chr3:51532096..51536424-chr3:51702408..51707498,7	K562	blood:
9	chr3:51428575..51432934-chr3:51531325..51537191,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000179837	Chromatin interaction
ENSG00000145050	Chromatin interaction
ENSG00000164080	Chromatin interaction
ENSG00000164081	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11716246	0.80[ASN][1000 genomes]
rs56175329	0.80[ASN][1000 genomes]
rs62257558	0.81[EUR][1000 genomes]
rs6773188	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7623949	HEMK1	cis	cerebellum	SCAN
rs7623949	AMIGO3	cis	cerebellum	SCAN
rs7623949	MST1	cis	cerebellum	SCAN
rs7623949	RAD54L2	cis	cerebellum	SCAN
rs7623949	DOCK3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51526200-51533200	Weak transcription	Small Intestine	intestine
2	chr3:51526200-51533200	Weak transcription	Spleen	Spleen
3	chr3:51529800-51533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:51532400-51533200	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr3:51532400-51533200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:51532400-51534400	Active TSS	Hela-S3	cervix
7	chr3:51532400-51534800	Active TSS	Psoas Muscle	Psoas
8	chr3:51532600-51533200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:51532600-51533200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:51532600-51533200	Flanking Active TSS	Dnd41	blood
11	chr3:51532600-51533200	Flanking Active TSS	Osteobl	bone
12	chr3:51532600-51533400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr3:51532600-51533400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr3:51532600-51533400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:51532600-51534400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:51532600-51534400	Active TSS	HMEC	breast
17	chr3:51532600-51534400	Active TSS	K562	blood
18	chr3:51532600-51534600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:51532600-51534600	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr3:51532600-51534600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:51532600-51534600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr3:51532600-51534600	Active TSS	GM12878-XiMat	blood
23	chr3:51532600-51534800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:51532600-51534800	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr3:51532600-51534800	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr3:51532600-51534800	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr3:51532600-51534800	Active TSS	A549	lung
28	chr3:51532800-51533200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:51532800-51533200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr3:51532800-51533200	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr3:51532800-51533200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:51532800-51533200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr3:51532800-51533200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:51532800-51533200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr3:51532800-51533200	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr3:51532800-51533200	Flanking Active TSS	Liver	Liver
37	chr3:51532800-51533200	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr3:51532800-51533200	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr3:51532800-51533200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr3:51532800-51533200	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr3:51532800-51533200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr3:51532800-51533200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr3:51532800-51533200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr3:51532800-51533200	Flanking Active TSS	Fetal Heart	heart
45	chr3:51532800-51533200	Flanking Active TSS	Fetal Thymus	thymus
46	chr3:51532800-51533200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr3:51532800-51533200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr3:51532800-51533200	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr3:51532800-51533200	Flanking Active TSS	HUVEC	blood vessel
50	chr3:51532800-51533400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links