Variant report

Variant	rs10982448
Chromosome Location	chr9:117672244-117672245
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	chr4:3387607..3388365-chr9:117671645..117672374,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10118244	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs10124990	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs10817681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10982443	0.96[EUR][1000 genomes]
rs1108983	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3181192	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs3181194	0.85[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs3181346	0.82[CEU][hapmap];0.91[YRI][hapmap];0.92[EUR][1000 genomes]
rs3181349	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181350	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181353	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181357	0.85[AFR][1000 genomes]
rs3181359	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181360	0.92[AFR][1000 genomes]
rs3181362	0.85[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs3789882	0.85[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs4978612	0.92[AFR][1000 genomes]
rs61024439	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6478118	0.85[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs7028089	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7854103	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7868670	0.88[AFR][1000 genomes]
rs7871914	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831695	chr9:117567626-117726247	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893767	chr9:117627569-117689838	Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117662200-117676200	Weak transcription	Gastric	stomach
2	chr9:117663400-117672800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr9:117663600-117672400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr9:117665800-117672800	Weak transcription	Spleen	Spleen
5	chr9:117667400-117673600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr9:117667600-117673200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:117667800-117683600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr9:117668800-117673400	Enhancers	Primary B cells from peripheral blood	blood
9	chr9:117668800-117673400	Enhancers	HMEC	breast
10	chr9:117669000-117674000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr9:117669200-117673200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:117669200-117673800	Enhancers	Fetal Thymus	thymus
13	chr9:117669400-117672400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
14	chr9:117669800-117672600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr9:117669800-117672800	Weak transcription	Fetal Stomach	stomach
16	chr9:117669800-117673600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr9:117670200-117672600	Enhancers	GM12878-XiMat	blood
18	chr9:117670200-117673600	Enhancers	Osteobl	bone
19	chr9:117670400-117672600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr9:117670400-117673400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:117670800-117672600	Weak transcription	HSMM	muscle
22	chr9:117670800-117673800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr9:117670800-117674200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr9:117670800-117687200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:117671000-117673000	Enhancers	Primary B cells from cord blood	blood
26	chr9:117671000-117673200	Genic enhancers	Primary T cells from cord blood	blood
27	chr9:117671000-117674600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:117671200-117672800	Weak transcription	Esophagus	oesophagus
29	chr9:117671200-117674200	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr9:117671200-117676800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:117671400-117672800	Weak transcription	NHDF-Ad	bronchial
32	chr9:117671400-117673200	Weak transcription	NHLF	lung
33	chr9:117671400-117674000	Enhancers	Hela-S3	cervix
34	chr9:117671400-117674200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:117671600-117672800	Weak transcription	HSMMtube	muscle
36	chr9:117671600-117673000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:117671600-117673200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:117671600-117673400	Weak transcription	NH-A	brain
39	chr9:117671600-117674000	Enhancers	A549	lung
40	chr9:117671600-117675000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr9:117671800-117672800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:117671800-117672800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:117671800-117673200	Genic enhancers	Thymus	Thymus
44	chr9:117671800-117674800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:117671800-117676600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:117671800-117676800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr9:117672000-117672400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:117672000-117672400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:117672000-117674400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr9:117672000-117674400	Enhancers	Dnd41	blood

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