Variant report

Variant	rs3825533
Chromosome Location	chr13:30781642-30781643
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	chr13:30780598..30783171-chr13:31037379..31039665,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189403	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12866391	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12871218	0.82[ASN][1000 genomes]
rs12874795	0.82[ASN][1000 genomes]
rs17632858	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2031998	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2149970	0.86[ASN][1000 genomes]
rs2149971	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2149973	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs34883025	0.82[ASN][1000 genomes]
rs34894712	0.82[ASN][1000 genomes]
rs35331241	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35963596	0.81[EUR][1000 genomes]
rs3803272	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4385994	0.82[ASN][1000 genomes]
rs61946958	0.81[EUR][1000 genomes]
rs7328946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9550538	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs9550539	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs9550540	0.81[EUR][1000 genomes]
rs9550541	0.81[EUR][1000 genomes]
rs9551867	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9551868	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9551875	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs9551879	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[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	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30754000-30798800	Weak transcription	Brain Anterior Caudate	brain
2	chr13:30760800-30781800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr13:30761600-30792800	Weak transcription	Fetal Brain Male	brain
4	chr13:30763600-30786400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr13:30764600-30790200	Weak transcription	Colon Smooth Muscle	Colon
6	chr13:30765600-30807000	Weak transcription	Gastric	stomach
7	chr13:30766000-30781800	Weak transcription	NH-A	brain
8	chr13:30766000-30783400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:30766200-30790400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:30766400-30804400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr13:30768000-30795000	Weak transcription	Brain Germinal Matrix	brain
12	chr13:30768600-30792600	Weak transcription	Spleen	Spleen
13	chr13:30768600-30798800	Weak transcription	HMEC	breast
14	chr13:30769000-30796400	Weak transcription	A549	lung
15	chr13:30769800-30790400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:30770000-30790400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr13:30770000-30790400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr13:30770000-30799200	Weak transcription	HSMMtube	muscle
19	chr13:30770400-30784400	Weak transcription	Psoas Muscle	Psoas
20	chr13:30770400-30786400	Weak transcription	Fetal Brain Female	brain
21	chr13:30770400-30790400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr13:30770600-30782000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr13:30770600-30786000	Weak transcription	Fetal Stomach	stomach
24	chr13:30770600-30786400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr13:30770600-30790400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:30770600-30796200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr13:30770600-30803200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr13:30771000-30782000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr13:30771200-30790200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr13:30771200-30790400	Weak transcription	Right Ventricle	heart
31	chr13:30771800-30794800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr13:30772400-30796400	Weak transcription	NHEK	skin
33	chr13:30773000-30782600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr13:30773400-30790400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr13:30774000-30796400	Weak transcription	Liver	Liver
36	chr13:30774200-30790400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr13:30774200-30796000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr13:30774400-30787200	Strong transcription	Dnd41	blood
39	chr13:30774400-30812600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr13:30774600-30790400	Weak transcription	Aorta	Aorta
41	chr13:30774600-30790400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:30774600-30795800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr13:30774600-30802800	Weak transcription	Lung	lung
44	chr13:30774600-30805200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:30775000-30790600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr13:30775000-30803000	Weak transcription	Esophagus	oesophagus
47	chr13:30775400-30783600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr13:30775600-30796600	Weak transcription	Fetal Kidney	kidney
49	chr13:30775800-30796600	Weak transcription	K562	blood
50	chr13:30776000-30790200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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