Variant report

Variant	rs56096139
Chromosome Location	chr16:69563412-69563413
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:69561937..69564667-chr16:70285129..70286658,2	MCF-7	breast:
2	chr16:69441221..69442807-chr16:69563296..69565834,2	K562	blood:
3	chr16:69492037..69494585-chr16:69563234..69566280,3	K562	blood:
4	chr16:69563250..69565350-chr16:69571620..69573342,2	K562	blood:
5	chr16:69563236..69563998-chr2:242626169..242626798,2	HCT-116	colon:
6	chr1:154934019..154934711-chr16:69563218..69563999,2	HCT-116	colon:
7	chr16:69561206..69567755-chr16:69595684..69602877,15	K562	blood:
8	chr16:69440915..69442721-chr16:69563296..69565171,2	K562	blood:
9	chr16:69563142..69566271-chr16:69570461..69572776,3	MCF-7	breast:
10	chr16:69561256..69567897-chr16:69597498..69602280,7	MCF-7	breast:
11	chr16:69562466..69565005-chr16:69568063..69569909,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163348	Chromatin interaction
ENSG00000223496	Chromatin interaction
ENSG00000223109	Chromatin interaction
ENSG00000102908	Chromatin interaction
ENSG00000271380	Chromatin interaction
ENSG00000168393	Chromatin interaction
ENSG00000132604	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12923231	0.95[ASN][1000 genomes]
rs12929503	0.97[ASN][1000 genomes]
rs12933292	0.97[ASN][1000 genomes]
rs13330951	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2032912	0.94[ASN][1000 genomes]
rs4783721	0.86[ASN][1000 genomes]
rs62052815	0.90[ASN][1000 genomes]
rs62052816	0.97[ASN][1000 genomes]
rs889398	0.95[ASN][1000 genomes]
rs889399	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv906821	chr16:69509506-69576894	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69555800-69563600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr16:69556200-69563600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr16:69558600-69563600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr16:69561000-69564400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr16:69561200-69564400	Weak transcription	Spleen	Spleen
6	chr16:69561400-69564000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr16:69561600-69563600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr16:69562400-69565800	Enhancers	Placenta	Placenta
9	chr16:69562600-69563600	Enhancers	Hela-S3	cervix
10	chr16:69562600-69564000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr16:69562600-69564400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr16:69562600-69564400	Enhancers	HSMMtube	muscle
13	chr16:69563000-69564400	Enhancers	H9 Cell Line	embryonic stem cell
14	chr16:69563000-69564400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr16:69563000-69564400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:69563000-69564400	Enhancers	NHEK	skin
17	chr16:69563000-69564600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr16:69563200-69563600	Weak transcription	Lung	lung
19	chr16:69563200-69563600	Enhancers	K562	blood
20	chr16:69563200-69564000	Flanking Active TSS	A549	lung
21	chr16:69563200-69564200	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr16:69563200-69564400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr16:69563200-69564400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr16:69563200-69564400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr16:69563200-69564400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr16:69563200-69564400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr16:69563200-69564400	Enhancers	HMEC	breast
28	chr16:69563200-69564600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr16:69563200-69564800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr16:69563200-69564800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr16:69563200-69565000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr16:69563200-69565200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr16:69563200-69565200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr16:69563200-69565200	Enhancers	HepG2	liver
35	chr16:69563200-69565200	Enhancers	HSMM	muscle
36	chr16:69563200-69565200	Enhancers	NH-A	brain
37	chr16:69563200-69565800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr16:69563200-69566400	Enhancers	NHDF-Ad	bronchial
39	chr16:69563400-69563800	Enhancers	Fetal Intestine Large	intestine
40	chr16:69563400-69564400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr16:69563400-69564400	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr16:69563400-69564400	Enhancers	Osteobl	bone
43	chr16:69563400-69565200	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr16:69563400-69565200	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr16:69563400-69565200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr16:69563400-69565200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr16:69563400-69566200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links