Variant report

Variant	rs60949675
Chromosome Location	chr3:47119511-47119512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47098199..47100265-chr3:47118377..47121357,2	MCF-7	breast:
2	chr3:47113958..47116821-chr3:47117778..47119607,2	K562	blood:
3	chr3:47117444..47119975-chr3:47141387..47143617,2	K562	blood:
4	chr3:47118002..47122103-chr3:47123133..47127114,5	K562	blood:

Variant related genes	Relation type
ENSG00000181555	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1109497	0.89[AMR][1000 genomes]
rs17079336	0.89[AMR][1000 genomes]
rs58906143	1.00[AMR][1000 genomes]
rs60579303	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60811415	0.89[AMR][1000 genomes]
rs6442058	1.00[AMR][1000 genomes]
rs6768374	1.00[AMR][1000 genomes]
rs6772269	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6809110	1.00[AMR][1000 genomes]
rs72895783	1.00[AMR][1000 genomes]
rs72913651	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72913679	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	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
5	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47078000-47130600	Weak transcription	Stomach Mucosa	stomach
2	chr3:47079600-47123800	Weak transcription	Pancreas	Pancrea
3	chr3:47079600-47124200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47079800-47124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:47083200-47135200	Weak transcription	Small Intestine	intestine
6	chr3:47083400-47138600	Weak transcription	Psoas Muscle	Psoas
7	chr3:47093400-47122600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:47093800-47123400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr3:47094200-47123800	Weak transcription	Esophagus	oesophagus
10	chr3:47095800-47121000	Weak transcription	Fetal Brain Male	brain
11	chr3:47098800-47121800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:47098800-47122000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:47098800-47122000	Weak transcription	Aorta	Aorta
14	chr3:47098800-47149600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:47099000-47121600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:47099000-47121800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:47099000-47121800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:47099000-47121800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:47099000-47122000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:47099000-47122000	Weak transcription	Gastric	stomach
21	chr3:47099000-47125200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:47099000-47128200	Weak transcription	Spleen	Spleen
23	chr3:47099200-47122000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:47100000-47122200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:47101000-47125200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:47101200-47123800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:47101400-47147800	Strong transcription	Dnd41	blood
28	chr3:47101600-47123800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:47101800-47121800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:47103800-47122000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:47105000-47121800	Weak transcription	HMEC	breast
32	chr3:47106200-47121800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:47106800-47121600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:47106800-47121600	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:47107000-47121800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:47107600-47122000	Weak transcription	Ovary	ovary
37	chr3:47107800-47121600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:47108000-47121800	Weak transcription	Brain Germinal Matrix	brain
39	chr3:47108000-47121800	Weak transcription	Colonic Mucosa	Colon
40	chr3:47108000-47122000	Weak transcription	Lung	lung
41	chr3:47108000-47125000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:47108200-47121400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:47108800-47120200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:47110200-47150200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:47110400-47133200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr3:47110600-47131600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:47110600-47148000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:47110800-47125200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr3:47111000-47147600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:47111800-47132400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links