Variant report

Variant	rs12458564
Chromosome Location	chr18:29600328-29600329
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29599759..29602632-chr18:29612702..29615585,2	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12455890	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162379	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4799624	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4799626	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7226474	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7230885	0.80[ASN][1000 genomes]
rs7236547	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

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	nsv1065285	chr18:29527884-29614986	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv1803283	chr18:29591102-29640430	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29597400-29600400	Flanking Active TSS	Dnd41	blood
2	chr18:29597600-29600600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr18:29597800-29600400	Active TSS	Rectal Smooth Muscle	rectum
4	chr18:29597800-29600600	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr18:29597800-29600600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr18:29597800-29600800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr18:29597800-29601000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr18:29598000-29600600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr18:29598000-29600600	Active TSS	Right Atrium	heart
10	chr18:29598000-29603200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr18:29598200-29600600	Active TSS	Brain Angular Gyrus	brain
12	chr18:29598400-29600400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr18:29598400-29600400	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr18:29598400-29600400	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr18:29598400-29600400	Active TSS	Fetal Intestine Small	intestine
16	chr18:29598400-29600400	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr18:29598400-29601000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr18:29598600-29600400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr18:29598600-29600600	Active TSS	Duodenum Mucosa	Duodenum
20	chr18:29598600-29600800	Active TSS	Thymus	Thymus
21	chr18:29598600-29601400	Active TSS	Primary T cells from cord blood	blood
22	chr18:29599000-29600400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr18:29599000-29600400	Active TSS	Primary T cells fromperipheralblood	blood
24	chr18:29599600-29600400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr18:29599600-29600600	Active TSS	Left Ventricle	heart
26	chr18:29599600-29600800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr18:29599600-29629600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr18:29599800-29600400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr18:29599800-29600400	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr18:29599800-29600400	Active TSS	Fetal Muscle Trunk	muscle
31	chr18:29599800-29600400	Active TSS	Fetal Muscle Leg	muscle
32	chr18:29599800-29600400	Active TSS	Placenta	Placenta
33	chr18:29599800-29600400	Active TSS	Right Ventricle	heart
34	chr18:29599800-29600400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
35	chr18:29599800-29600600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
36	chr18:29599800-29600600	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr18:29599800-29600800	Weak transcription	Small Intestine	intestine
38	chr18:29599800-29601000	Active TSS	Psoas Muscle	Psoas
39	chr18:29599800-29601800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr18:29599800-29602400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr18:29600000-29600400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr18:29600000-29600400	Enhancers	Stomach Mucosa	stomach
43	chr18:29600000-29600400	Active TSS	GM12878-XiMat	blood
44	chr18:29600000-29600600	Enhancers	Primary B cells from peripheral blood	blood
45	chr18:29600000-29600600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr18:29600000-29601400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr18:29600000-29601400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr18:29600000-29601400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr18:29600000-29601400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr18:29600000-29601400	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links