Variant report

Variant	rs9551744
Chromosome Location	chr13:30384052-30384053
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	chr13:30382188..30384280-chr13:31038768..31041039,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189403	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1058650	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11147398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12872400	0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1323931	0.87[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1410110	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1772727	0.82[AFR][1000 genomes]
rs1854176	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1886170	0.91[YRI][hapmap]
rs1927193	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2025604	0.82[ASN][1000 genomes]
rs2182129	0.87[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2234416	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2388244	0.87[YRI][hapmap]
rs2388246	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2388247	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2761938	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2761939	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2761940	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278034	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278037	0.91[YRI][hapmap]
rs35541102	0.87[ASN][1000 genomes]
rs4083610	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4238128	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4265673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4297554	0.88[ASN][1000 genomes]
rs4769772	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4769774	0.91[YRI][hapmap]
rs4769775	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6490429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6490430	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7320474	0.88[ASN][1000 genomes]
rs7326253	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7330356	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7335148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7342470	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs765404	0.82[ASN][1000 genomes]
rs7981622	0.85[ASN][1000 genomes]
rs7995666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9314972	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9314973	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9314974	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9314978	0.88[ASN][1000 genomes]
rs9506226	0.87[ASN][1000 genomes]
rs9506229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9506230	0.85[AFR][1000 genomes]
rs9506231	0.87[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs9506233	0.85[ASN][1000 genomes]
rs9508550	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9508553	0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9508554	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9508555	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs9508557	0.88[ASN][1000 genomes]
rs9508558	0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9508559	0.87[ASN][1000 genomes]
rs9508560	0.85[ASN][1000 genomes]
rs9508561	0.80[ASN][1000 genomes]
rs9508564	0.85[ASN][1000 genomes]
rs9508568	0.91[ASN][1000 genomes]
rs9550494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9551739	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9551751	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9578136	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9578139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30363800-30385000	Weak transcription	Left Ventricle	heart
2	chr13:30376200-30384200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr13:30376400-30386000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr13:30376600-30385200	Weak transcription	Lung	lung
5	chr13:30376600-30385600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr13:30376600-30420600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr13:30377400-30390000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:30377600-30384400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr13:30377800-30384600	Weak transcription	Osteobl	bone
10	chr13:30378000-30391800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr13:30378800-30384800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr13:30380600-30384600	Enhancers	Liver	Liver
13	chr13:30380600-30386800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:30381000-30384200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr13:30381000-30384600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr13:30381000-30384600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr13:30381200-30385800	Enhancers	Brain Angular Gyrus	brain
18	chr13:30381400-30384200	Weak transcription	Brain Germinal Matrix	brain
19	chr13:30381400-30384400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr13:30381400-30385600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr13:30381400-30386600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr13:30381400-30386800	Enhancers	Stomach Mucosa	stomach
23	chr13:30381600-30384200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr13:30381600-30384400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr13:30381600-30384800	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr13:30381600-30390600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr13:30382600-30388000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:30382600-30388800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr13:30382600-30390800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr13:30382800-30385800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr13:30383200-30384200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr13:30383200-30384200	Enhancers	Ovary	ovary
33	chr13:30383200-30385000	Enhancers	Adipose Nuclei	Adipose
34	chr13:30383200-30385600	Enhancers	Brain Cingulate Gyrus	brain
35	chr13:30383200-30385800	Enhancers	Brain Anterior Caudate	brain
36	chr13:30383200-30385800	Enhancers	Brain Hippocampus Middle	brain
37	chr13:30383200-30385800	Enhancers	Fetal Heart	heart
38	chr13:30383200-30385800	Enhancers	Small Intestine	intestine
39	chr13:30383200-30386000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr13:30383200-30386200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr13:30383200-30386600	Enhancers	HepG2	liver
42	chr13:30383400-30384600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr13:30383400-30384800	Enhancers	GM12878-XiMat	blood
44	chr13:30383400-30385600	Enhancers	Fetal Lung	lung
45	chr13:30383400-30385800	Enhancers	Duodenum Mucosa	Duodenum
46	chr13:30383400-30385800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr13:30383400-30386000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr13:30383600-30384400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr13:30383600-30384400	Weak transcription	Fetal Intestine Large	intestine
50	chr13:30383600-30385600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links