Variant report

Variant	rs9568649
Chromosome Location	chr13:52245973-52245974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52238827..52243045-chr13:52243097..52246375,4	MCF-7	breast:
2	chr13:52024317..52027530-chr13:52243525..52246255,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17075902	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803201	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825410	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4075628	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4625625	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4941710	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4943018	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7328589	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7328695	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7333623	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7986066	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9563065	0.87[ASN][1000 genomes]
rs9563066	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9563067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568644	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9568647	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568650	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568653	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][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	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52219600-52253800	Weak transcription	Psoas Muscle	Psoas
2	chr13:52220400-52259000	Weak transcription	Thymus	Thymus
3	chr13:52221200-52253800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr13:52228400-52247000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr13:52228600-52248000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:52228600-52254000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:52229000-52248400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:52231600-52249600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr13:52232200-52261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr13:52232800-52256400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr13:52234000-52277800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr13:52234200-52258800	Weak transcription	Adipose Nuclei	Adipose
13	chr13:52234200-52263200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr13:52234800-52257600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr13:52235200-52253800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr13:52236600-52248600	Weak transcription	Lung	lung
17	chr13:52237200-52257400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr13:52237200-52261400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr13:52237400-52254400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr13:52237600-52248200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr13:52238400-52250000	Weak transcription	Primary T cells from cord blood	blood
22	chr13:52238600-52247400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr13:52238600-52248400	Weak transcription	Left Ventricle	heart
24	chr13:52238600-52249600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr13:52238600-52256800	Weak transcription	Fetal Muscle Leg	muscle
26	chr13:52238600-52259400	Weak transcription	Fetal Stomach	stomach
27	chr13:52238800-52247400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr13:52239200-52257400	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:52239200-52263200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr13:52240200-52247400	Weak transcription	HMEC	breast
31	chr13:52240400-52250200	Weak transcription	Gastric	stomach
32	chr13:52240800-52247000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:52240800-52247200	Weak transcription	Fetal Lung	lung
34	chr13:52240800-52247200	Weak transcription	NHEK	skin
35	chr13:52240800-52248400	Weak transcription	Aorta	Aorta
36	chr13:52240800-52248400	Weak transcription	Esophagus	oesophagus
37	chr13:52240800-52248400	Weak transcription	Pancreas	Pancrea
38	chr13:52240800-52249200	Weak transcription	Primary B cells from cord blood	blood
39	chr13:52240800-52250000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:52240800-52254000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:52241200-52247200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr13:52241400-52246600	Weak transcription	Hela-S3	cervix
43	chr13:52241400-52248400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr13:52241400-52248400	Weak transcription	Brain Angular Gyrus	brain
45	chr13:52241600-52247400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr13:52243200-52247000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr13:52243400-52247200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr13:52243400-52248400	Weak transcription	Stomach Mucosa	stomach
49	chr13:52243400-52249200	Enhancers	HepG2	liver
50	chr13:52243400-52254000	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links