Variant report

Variant	rs9578139
Chromosome Location	chr13:30386310-30386311
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	chr13:30386203..30387833-chr13:30389830..30392025,3	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1058650	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11147398	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12872400	0.82[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1323931	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1410110	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854176	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1927193	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2025604	0.84[ASN][1000 genomes]
rs2182129	0.87[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2234416	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2388246	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2388247	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2487664	0.85[AFR][1000 genomes]
rs2761938	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761939	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2761940	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs278034	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2892463	0.86[YRI][hapmap]
rs35541102	0.89[ASN][1000 genomes]
rs4083610	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238128	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4265673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4297554	0.91[ASN][1000 genomes]
rs4769772	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4769775	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6490429	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490430	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72623487	0.80[ASN][1000 genomes]
rs7320474	0.91[ASN][1000 genomes]
rs7326253	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330356	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7335148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342470	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs765404	0.84[ASN][1000 genomes]
rs7981622	0.87[ASN][1000 genomes]
rs7995666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9314972	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9314973	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9314974	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9314978	0.91[ASN][1000 genomes]
rs9506226	0.89[ASN][1000 genomes]
rs9506229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9506231	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs9506233	0.87[ASN][1000 genomes]
rs9508550	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9508553	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9508554	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9508557	0.91[ASN][1000 genomes]
rs9508558	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9508559	0.89[ASN][1000 genomes]
rs9508560	0.85[ASN][1000 genomes]
rs9508564	0.87[ASN][1000 genomes]
rs9508568	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9550494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9551739	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9551741	0.81[ASN][1000 genomes]
rs9551744	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]
rs9551751	0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9578136	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30376600-30420600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr13:30377400-30390000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr13:30378000-30391800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr13:30380600-30386800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr13:30381400-30386600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:30381400-30386800	Enhancers	Stomach Mucosa	stomach
7	chr13:30381600-30390600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr13:30382600-30388000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr13:30382600-30388800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr13:30382600-30390800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr13:30383200-30386600	Enhancers	HepG2	liver
12	chr13:30383600-30389200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr13:30384600-30386400	Enhancers	Ovary	ovary
14	chr13:30384800-30387600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:30384800-30389600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr13:30385000-30391400	Weak transcription	Osteobl	bone
17	chr13:30385200-30386600	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr13:30385200-30386800	Enhancers	Liver	Liver
19	chr13:30385200-30389200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:30385200-30391200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr13:30385400-30387600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr13:30385400-30389400	Weak transcription	Colon Smooth Muscle	Colon
23	chr13:30385600-30386400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr13:30385600-30387200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr13:30385600-30387600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr13:30385600-30390400	Weak transcription	GM12878-XiMat	blood
27	chr13:30385600-30391400	Weak transcription	Brain Germinal Matrix	brain
28	chr13:30385800-30387400	Weak transcription	Brain Angular Gyrus	brain
29	chr13:30385800-30387400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:30385800-30387800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr13:30385800-30387800	Weak transcription	Brain Substantia Nigra	brain
32	chr13:30385800-30388600	Weak transcription	Left Ventricle	heart
33	chr13:30385800-30389600	Weak transcription	Brain Anterior Caudate	brain
34	chr13:30385800-30390600	Weak transcription	Gastric	stomach
35	chr13:30385800-30390600	Weak transcription	Psoas Muscle	Psoas
36	chr13:30385800-30391200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr13:30385800-30391800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr13:30385800-30403000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr13:30385800-30406800	Weak transcription	Pancreas	Pancrea
40	chr13:30385800-30410600	Weak transcription	Small Intestine	intestine
41	chr13:30386000-30386400	Enhancers	Brain Hippocampus Middle	brain
42	chr13:30386000-30386600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr13:30386000-30389200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr13:30386000-30390600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr13:30386000-30390600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr13:30386000-30391000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr13:30386000-30391000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr13:30386000-30391400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr13:30386000-30406200	Weak transcription	Fetal Intestine Small	intestine
50	chr13:30386200-30386400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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