Variant report

Variant	rs13338560
Chromosome Location	chr16:69605498-69605499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69598845..69601528-chr16:69603220..69607437,4	MCF-7	breast:
2	chr16:69604663..69607027-chr16:69622844..69624484,2	K562	blood:
3	chr16:69603757..69608003-chr16:69608189..69613154,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102908	Chromatin interaction
ENSG00000223109	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10517	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1142105	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12102305	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12921017	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13329844	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13331055	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13331216	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13335277	0.88[EUR][1000 genomes]
rs13335317	0.88[EUR][1000 genomes]
rs13335664	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16958965	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16958997	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16959059	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2304526	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28392989	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28473508	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28637633	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2917665	0.84[AMR][1000 genomes]
rs2917667	0.84[AMR][1000 genomes]
rs2917669	0.80[AMR][1000 genomes]
rs2917673	0.84[AMR][1000 genomes]
rs2917674	0.80[AMR][1000 genomes]
rs2965752	0.84[AMR][1000 genomes]
rs3785075	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3826154	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3926183	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61628167	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs689452	0.84[AMR][1000 genomes]
rs689456	0.84[AMR][1000 genomes]
rs7200420	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7359387	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9888993	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9924264	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9924953	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9925037	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9927809	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9934321	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9934681	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9936464	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9937018	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9938717	0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1852	chr16:69566121-69610962	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69601400-69613000	Weak transcription	Small Intestine	intestine
2	chr16:69601600-69610600	Weak transcription	Ovary	ovary
3	chr16:69601800-69610600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:69602000-69606000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr16:69602000-69610600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr16:69602000-69633000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr16:69602200-69605600	Weak transcription	Colonic Mucosa	Colon
8	chr16:69602200-69609200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:69602200-69610400	Weak transcription	Placenta	Placenta
10	chr16:69602200-69610400	Weak transcription	Lung	lung
11	chr16:69602200-69619400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr16:69602200-69622000	Weak transcription	Gastric	stomach
13	chr16:69602200-69627000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr16:69602200-69628600	Weak transcription	Right Atrium	heart
15	chr16:69602200-69631600	Weak transcription	Pancreas	Pancrea
16	chr16:69602200-69643200	Weak transcription	Fetal Muscle Leg	muscle
17	chr16:69602200-69646600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr16:69602200-69653600	Weak transcription	Fetal Thymus	thymus
19	chr16:69602400-69605600	Strong transcription	HSMM	muscle
20	chr16:69602400-69610400	Weak transcription	Psoas Muscle	Psoas
21	chr16:69602600-69607600	Weak transcription	Fetal Intestine Small	intestine
22	chr16:69602600-69609000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:69602600-69610600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr16:69602600-69614200	Weak transcription	Fetal Stomach	stomach
25	chr16:69602600-69628600	Weak transcription	Thymus	Thymus
26	chr16:69602600-69628800	Weak transcription	Right Ventricle	heart
27	chr16:69602600-69629600	Weak transcription	HSMMtube	muscle
28	chr16:69602600-69630200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr16:69602600-69630800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr16:69602800-69605600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr16:69602800-69608800	Weak transcription	Fetal Intestine Large	intestine
32	chr16:69602800-69610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr16:69602800-69611400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr16:69602800-69627800	Weak transcription	Fetal Kidney	kidney
35	chr16:69602800-69629200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr16:69603000-69610600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr16:69603000-69613400	Weak transcription	Fetal Heart	heart
38	chr16:69603000-69617400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr16:69603000-69627800	Weak transcription	Brain Substantia Nigra	brain
40	chr16:69603000-69647400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr16:69603200-69606200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr16:69603200-69606800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:69603200-69610600	Weak transcription	Brain Angular Gyrus	brain
44	chr16:69603200-69612000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr16:69603200-69627800	Weak transcription	Primary B cells from cord blood	blood
46	chr16:69603200-69629600	Weak transcription	NH-A	brain
47	chr16:69603400-69614600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr16:69603400-69617200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr16:69603400-69623600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr16:69603600-69606000	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links