Variant report

Variant	rs12553869
Chromosome Location	chr9:97748308-97748309
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97674046..97692471-chr9:97747275..97760115,80	MCF-7	breast:
2	chr9:97685386..97687734-chr9:97748226..97751187,2	MCF-7	breast:
3	chr9:97746218..97749108-chr9:97765101..97767458,4	K562	blood:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1020962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1038092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10761371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10993471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12552838	1.00[CEU][hapmap]
rs12554454	1.00[CEU][hapmap]
rs12555128	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12555829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1564235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1571896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16911834	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16911856	1.00[JPT][hapmap]
rs1871220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1888944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1888945	0.96[ASN][1000 genomes]
rs1888946	0.96[ASN][1000 genomes]
rs2061798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2061801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2104888	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs2306207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3739748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3780560	1.00[JPT][hapmap]
rs4743975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4743977	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4743978	0.96[ASN][1000 genomes]
rs4743989	1.00[JPT][hapmap]
rs4744421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4744429	0.96[ASN][1000 genomes]
rs4744437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4744440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs475413	1.00[JPT][hapmap]
rs67134693	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022963	1.00[JPT][hapmap]
rs7039768	0.96[ASN][1000 genomes]
rs7046900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs72750335	1.00[ASN][1000 genomes]
rs72750346	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72750351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750367	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72750373	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73540087	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97713800-97757400	Weak transcription	Fetal Brain Female	brain
3	chr9:97715000-97758200	Weak transcription	Spleen	Spleen
4	chr9:97715400-97749600	Weak transcription	Thymus	Thymus
5	chr9:97728000-97754200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:97733400-97757600	Weak transcription	Esophagus	oesophagus
7	chr9:97734600-97757600	Weak transcription	Gastric	stomach
8	chr9:97736600-97757200	Weak transcription	NH-A	brain
9	chr9:97736600-97757400	Weak transcription	NHLF	lung
10	chr9:97736600-97757600	Weak transcription	Adipose Nuclei	Adipose
11	chr9:97736600-97757600	Weak transcription	Osteobl	bone
12	chr9:97736600-97766200	Weak transcription	Right Ventricle	heart
13	chr9:97737000-97757200	Weak transcription	Fetal Heart	heart
14	chr9:97737000-97758200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:97738000-97757600	Weak transcription	Lung	lung
16	chr9:97738200-97757600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:97738600-97749200	Weak transcription	Ovary	ovary
18	chr9:97738600-97753600	Weak transcription	Fetal Lung	lung
19	chr9:97738600-97757200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:97738600-97757400	Weak transcription	Left Ventricle	heart
21	chr9:97738600-97757600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr9:97738800-97754800	Weak transcription	NHDF-Ad	bronchial
23	chr9:97740200-97758200	Weak transcription	Placenta	Placenta
24	chr9:97741200-97758200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:97742400-97753000	Weak transcription	Fetal Intestine Large	intestine
26	chr9:97742600-97757400	Weak transcription	Psoas Muscle	Psoas
27	chr9:97742600-97763200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:97742800-97754400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:97743000-97752600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:97743000-97757000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:97743200-97752000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:97743200-97757200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:97743200-97759200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr9:97743400-97751200	Weak transcription	Fetal Stomach	stomach
35	chr9:97743400-97757600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr9:97743600-97758200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr9:97743800-97749800	Weak transcription	Aorta	Aorta
38	chr9:97744000-97750600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:97744000-97751200	Weak transcription	Fetal Intestine Small	intestine
40	chr9:97744000-97757600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:97744000-97758200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:97744200-97757600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:97744200-97763200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:97744400-97754200	Weak transcription	Fetal Kidney	kidney
45	chr9:97744400-97757400	Weak transcription	Brain Angular Gyrus	brain
46	chr9:97744400-97757400	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:97744400-97757600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr9:97744800-97752000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:97744800-97754400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:97744800-97758200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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