Variant report

Variant	rs4664120
Chromosome Location	chr2:153501258-153501259
allele	C/T
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:153495600..153499231-chr2:153499718..153501941,4	MCF-7	breast:
2	chr2:153496498..153499473-chr2:153499493..153501534,3	K562	blood:
3	chr2:153500933..153503507-chr2:153514364..153517064,2	K562	blood:
4	chr2:153498882..153502328-chr2:153504598..153506576,3	K562	blood:
5	chr2:153501231..153504179-chr2:153533212..153536871,4	K562	blood:
6	chr2:153499674..153501480-chr2:153510390..153512975,2	K562	blood:
7	chr2:153498882..153503478-chr2:153504081..153508204,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196504	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10048775	0.82[EUR][1000 genomes]
rs10169433	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10178613	0.86[EUR][1000 genomes]
rs10193713	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12987348	1.00[CHB][hapmap]
rs12999189	1.00[CHB][hapmap]
rs13018434	1.00[CHB][hapmap]
rs13413144	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13419134	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13427289	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1437677	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16831151	1.00[CHB][hapmap]
rs2450	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4664599	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4664608	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56191709	0.86[EUR][1000 genomes]
rs62179597	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62179623	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62179635	0.80[EUR][1000 genomes]
rs62179636	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9989874	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3693437	chr2:153484685-153505003	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153457200-153505000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:153463800-153502800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:153464000-153502800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:153467200-153504000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:153469000-153509800	Weak transcription	Small Intestine	intestine
6	chr2:153471000-153507000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:153472000-153522000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:153474400-153505000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:153481200-153502200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:153481200-153502400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:153481400-153502400	Strong transcription	Placenta	Placenta
12	chr2:153481400-153503000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:153484400-153502600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:153484400-153503000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr2:153484400-153504200	Strong transcription	Fetal Muscle Leg	muscle
16	chr2:153486200-153503000	Strong transcription	Fetal Stomach	stomach
17	chr2:153487600-153505000	Weak transcription	Fetal Thymus	thymus
18	chr2:153488600-153503200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:153491600-153502800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:153491600-153504000	Strong transcription	HepG2	liver
21	chr2:153492000-153508200	Weak transcription	Primary B cells from cord blood	blood
22	chr2:153492200-153502600	Strong transcription	Lung	lung
23	chr2:153492200-153502800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:153492400-153502400	Strong transcription	NHEK	skin
25	chr2:153492400-153506200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:153492400-153513400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:153492600-153501400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:153492600-153501400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:153492600-153501800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:153492600-153502400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:153492600-153502400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:153492600-153502400	Strong transcription	HMEC	breast
33	chr2:153492800-153501400	Weak transcription	GM12878-XiMat	blood
34	chr2:153492800-153502200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:153492800-153502400	Strong transcription	Fetal Kidney	kidney
36	chr2:153492800-153502600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:153492800-153502600	Strong transcription	Brain Hippocampus Middle	brain
38	chr2:153492800-153502800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:153492800-153502800	Strong transcription	Fetal Brain Female	brain
40	chr2:153492800-153503400	Strong transcription	Fetal Intestine Large	intestine
41	chr2:153492800-153504400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:153492800-153504600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:153493000-153501600	Strong transcription	Fetal Lung	lung
44	chr2:153493000-153502600	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:153493000-153502800	Strong transcription	Adipose Nuclei	Adipose
46	chr2:153493000-153503000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:153493000-153503200	Strong transcription	Brain Substantia Nigra	brain
48	chr2:153493200-153502400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr2:153493200-153503200	Strong transcription	Brain Cingulate Gyrus	brain
50	chr2:153493400-153503000	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links