Variant report

Variant	rs2939538
Chromosome Location	chr5:145559988-145559989
allele	A/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: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	chr5:145559594..145562426-chr5:145581996..145584629,4	MCF-7	breast:
2	chr5:145549719..145552981-chr5:145557063..145560291,4	MCF-7	breast:
3	chr5:145559745..145561849-chr5:145588233..145589890,2	K562	blood:
4	chr5:145558307..145563846-chr5:145580315..145584343,10	K562	blood:
5	chr5:145555213..145560576-chr5:145560598..145562206,4	K562	blood:
6	chr5:145543973..145545500-chr5:145559065..145562026,2	K562	blood:
7	chr5:145559635..145562318-chr5:145826820..145828574,2	K562	blood:
8	chr5:145559635..145563527-chr5:145825770..145828320,3	K562	blood:
9	chr5:145558240..145560527-chr5:145600863..145603054,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000133706	Chromatin interaction
ENSG00000091009	Chromatin interaction
ENSG00000113649	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10491259	0.90[YRI][hapmap]
rs2063002	0.90[YRI][hapmap]
rs2939522	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2939526	1.00[AMR][1000 genomes]
rs2939534	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2939536	0.90[YRI][hapmap]
rs2939537	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962500	1.00[YRI][hapmap]
rs2962505	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962506	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962507	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962512	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962513	0.98[AFR][1000 genomes]
rs2962514	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962516	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963913	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963937	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4705440	0.90[AFR][1000 genomes]
rs6877277	0.90[YRI][hapmap]
rs7707229	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883006	chr5:145450586-145672431	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428128	chr5:145503978-145682880	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv883007	chr5:145506100-145672431	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv883008	chr5:145509728-145642925	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3348501	chr5:145543808-145572250	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145481200-145560200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:145491000-145560200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:145491200-145560200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:145491200-145560200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:145491200-145560800	Weak transcription	Stomach Mucosa	stomach
6	chr5:145491400-145560000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:145491400-145560400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:145492200-145560200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:145532200-145561000	Weak transcription	Esophagus	oesophagus
10	chr5:145537800-145560800	Weak transcription	Fetal Heart	heart
11	chr5:145541000-145560400	Weak transcription	Right Atrium	heart
12	chr5:145542600-145560200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:145542600-145560400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:145542600-145560600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:145542800-145561200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:145543000-145560200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:145543600-145560400	Weak transcription	Brain Angular Gyrus	brain
18	chr5:145544000-145560400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:145544000-145560400	Weak transcription	Psoas Muscle	Psoas
20	chr5:145546200-145560200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:145546200-145560400	Weak transcription	Pancreas	Pancrea
22	chr5:145547000-145561000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr5:145548000-145561000	Weak transcription	NHLF	lung
24	chr5:145550000-145561000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:145550400-145561000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:145550600-145560400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:145550600-145561000	Weak transcription	Colonic Mucosa	Colon
28	chr5:145550600-145561600	Weak transcription	Aorta	Aorta
29	chr5:145550600-145561600	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:145550800-145560400	Weak transcription	Right Ventricle	heart
31	chr5:145550800-145560400	Weak transcription	Spleen	Spleen
32	chr5:145550800-145560600	Weak transcription	Ovary	ovary
33	chr5:145550800-145561000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:145550800-145561000	Weak transcription	Fetal Kidney	kidney
35	chr5:145550800-145561000	Weak transcription	Fetal Lung	lung
36	chr5:145550800-145561000	Weak transcription	HSMMtube	muscle
37	chr5:145551000-145560400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:145551400-145560200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr5:145551600-145560200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr5:145551600-145560400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:145551600-145561000	Weak transcription	Brain Substantia Nigra	brain
42	chr5:145551800-145560200	Weak transcription	NHEK	skin
43	chr5:145551800-145560400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:145551800-145561000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr5:145551800-145561000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr5:145552600-145561000	Strong transcription	Fetal Stomach	stomach
47	chr5:145553400-145560400	Weak transcription	HUVEC	blood vessel
48	chr5:145553600-145560400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr5:145553600-145560800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:145553600-145561000	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links