Variant report

Variant	rs62348040
Chromosome Location	chr5:17227808-17227809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:17223199..17226233-chr5:17226952..17230155,3	MCF-7	breast:
2	chr5:17219335..17222848-chr5:17226972..17230280,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1105298	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2242415	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291236	0.96[ASN][1000 genomes]
rs4288115	0.83[ASN][1000 genomes]
rs7733967	0.96[ASN][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	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv830218	chr5:17093162-17290045	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17219800-17231800	Weak transcription	Fetal Kidney	kidney
2	chr5:17219800-17233600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:17220400-17229400	Weak transcription	Brain Anterior Caudate	brain
4	chr5:17221400-17228200	Weak transcription	HUVEC	blood vessel
5	chr5:17222600-17228800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:17222600-17228800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr5:17222800-17239000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:17223200-17235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:17223400-17229400	Weak transcription	Fetal Thymus	thymus
10	chr5:17223600-17230400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:17224200-17228600	Weak transcription	Ovary	ovary
12	chr5:17224400-17233400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:17225000-17228800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:17225200-17231800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:17225400-17228000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:17225400-17228200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:17225400-17228800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:17225400-17231000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:17225600-17228200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr5:17225600-17228600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:17225600-17228600	Weak transcription	HSMMtube	muscle
22	chr5:17225600-17232600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:17225600-17241600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr5:17225800-17228000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:17225800-17228200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:17225800-17228400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:17225800-17229000	Weak transcription	Fetal Muscle Leg	muscle
28	chr5:17225800-17229200	Weak transcription	Spleen	Spleen
29	chr5:17225800-17229400	Weak transcription	Placenta	Placenta
30	chr5:17225800-17229400	Weak transcription	Fetal Stomach	stomach
31	chr5:17225800-17232400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:17226000-17229400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:17226800-17228200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:17226800-17228600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:17226800-17228600	Enhancers	NHEK	skin
36	chr5:17227000-17228000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:17227000-17228000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:17227000-17228200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:17227000-17228200	Enhancers	GM12878-XiMat	blood
40	chr5:17227000-17228600	Weak transcription	Fetal Lung	lung
41	chr5:17227600-17228000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:17227600-17228000	Enhancers	Primary B cells from peripheral blood	blood
43	chr5:17227600-17228600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:17227800-17228000	Enhancers	Primary B cells from cord blood	blood
45	chr5:17227800-17228000	Enhancers	Fetal Brain Female	brain
46	chr5:17227800-17228000	Genic enhancers	A549	lung
47	chr5:17227800-17228000	Enhancers	NHLF	lung
48	chr5:17227800-17228200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:17227800-17228200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:17227800-17228400	Genic enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links