Variant report

Variant	rs62137039
Chromosome Location	chr2:48647407-48647408
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:48336922..48340984-chr2:48645140..48651052,10	MCF-7	breast:
2	chr2:48647192..48649423-chr2:48652404..48655156,2	MCF-7	breast:
3	chr2:48337553..48343006-chr2:48644200..48649231,9	MCF-7	breast:
4	chr2:48357074..48359129-chr2:48646502..48648468,2	MCF-7	breast:
5	chr2:48636349..48637908-chr2:48646875..48649366,2	MCF-7	breast:
6	chr2:48540164..48542701-chr2:48646519..48648183,2	MCF-7	breast:
7	chr2:48647311..48649443-chr2:48666220..48667845,2	MCF-7	breast:
8	chr2:48641901..48644739-chr2:48646186..48647771,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000170802	Chromatin interaction
ENSG00000162869	Chromatin interaction
ENSG00000272663	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17037329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17325537	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17397442	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57582834	0.94[AFR][1000 genomes]
rs60050318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60059816	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62137020	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62137023	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62137026	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62137044	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67567718	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72820456	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72822209	0.85[EUR][1000 genomes]
rs7583717	0.90[AMR][1000 genomes];0.88[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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48640400-48647600	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:48640400-48647600	Weak transcription	Ovary	ovary
3	chr2:48640600-48647800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:48642400-48647600	Weak transcription	Pancreas	Pancrea
5	chr2:48642800-48647600	Weak transcription	Osteobl	bone
6	chr2:48643000-48647600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:48643000-48647600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:48643000-48647600	Weak transcription	NHLF	lung
9	chr2:48643200-48647600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:48643200-48647600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:48643200-48647800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:48643400-48647600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:48643400-48647800	Weak transcription	Fetal Kidney	kidney
14	chr2:48643600-48647600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:48643600-48647600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:48643600-48647600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:48643600-48647600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:48643600-48647600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:48643600-48647600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:48643600-48647600	Weak transcription	Brain Germinal Matrix	brain
21	chr2:48643600-48647600	Weak transcription	Fetal Lung	lung
22	chr2:48643600-48651200	Weak transcription	Psoas Muscle	Psoas
23	chr2:48643800-48647600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:48643800-48647600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:48643800-48647600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:48643800-48647600	Weak transcription	Fetal Brain Female	brain
27	chr2:48643800-48647800	Weak transcription	Fetal Heart	heart
28	chr2:48643800-48647800	Weak transcription	HSMMtube	muscle
29	chr2:48644000-48647600	Weak transcription	GM12878-XiMat	blood
30	chr2:48645200-48651000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:48645400-48647600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:48645600-48647600	Weak transcription	Thymus	Thymus
33	chr2:48645800-48647600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:48645800-48647600	Weak transcription	Fetal Intestine Large	intestine
35	chr2:48645800-48647600	Weak transcription	Fetal Thymus	thymus
36	chr2:48645800-48648600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:48646000-48647600	Enhancers	HepG2	liver
38	chr2:48646200-48647600	Weak transcription	Fetal Intestine Small	intestine
39	chr2:48646400-48647600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:48646400-48647800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:48646600-48647600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:48646600-48648400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:48646600-48648400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:48646800-48648000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:48646800-48648200	Enhancers	Spleen	Spleen
46	chr2:48646800-48648400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr2:48646800-48648400	Enhancers	HMEC	breast
48	chr2:48647000-48647600	Bivalent Enhancer	Fetal Stomach	stomach
49	chr2:48647000-48647600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr2:48647000-48647800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links