Variant report

Variant	rs72918739
Chromosome Location	chr2:54752402-54752403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54752145..54754517-chr2:54758567..54761057,2	MCF-7	breast:
2	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:
3	chr2:54747821..54752887-chr2:54784386..54788690,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17045958	0.86[AFR][1000 genomes]
rs57749522	1.00[AMR][1000 genomes]
rs6709549	0.83[AFR][1000 genomes]
rs72906419	1.00[AMR][1000 genomes]
rs72911566	1.00[AMR][1000 genomes]
rs72915054	0.83[AFR][1000 genomes]
rs72918780	1.00[AMR][1000 genomes]
rs72918782	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
2	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
3	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
4	chr2:54740600-54753400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:54744400-54753400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:54744400-54753400	Weak transcription	Ovary	ovary
9	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
10	chr2:54744600-54753400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:54746600-54758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:54747200-54753200	Weak transcription	Fetal Brain Female	brain
14	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:54747400-54753600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:54747800-54753400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:54748200-54753600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
21	chr2:54749800-54752600	Enhancers	HMEC	breast
22	chr2:54750000-54752600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:54750000-54752600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:54750000-54752600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:54750200-54752800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:54750200-54753200	Enhancers	Fetal Heart	heart
27	chr2:54750400-54752600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:54750400-54753400	Enhancers	Brain Anterior Caudate	brain
29	chr2:54750400-54753600	Enhancers	Right Ventricle	heart
30	chr2:54750600-54752600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:54750600-54752600	Enhancers	Adipose Nuclei	Adipose
32	chr2:54750600-54752600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:54750600-54753600	Enhancers	Left Ventricle	heart
34	chr2:54750600-54757000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:54750800-54753200	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:54750800-54753200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr2:54750800-54753400	Weak transcription	Liver	Liver
38	chr2:54750800-54753600	Weak transcription	Brain Germinal Matrix	brain
39	chr2:54750800-54759200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:54751000-54753200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:54751000-54753200	Weak transcription	HepG2	liver
43	chr2:54751000-54753600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:54751000-54756800	Weak transcription	Fetal Intestine Large	intestine
45	chr2:54751000-54759400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:54751000-54759600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr2:54751000-54760200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:54751400-54752600	Enhancers	Psoas Muscle	Psoas
49	chr2:54751400-54752800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr2:54751600-54752600	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links