Variant report

Variant	rs9548835
Chromosome Location	chr13:40164648-40164649
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40154532..40156238-chr13:40163424..40165796,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1072605	0.87[AMR][1000 genomes]
rs1160321	0.81[CEU][hapmap]
rs2324342	0.92[EUR][1000 genomes]
rs2324343	0.92[EUR][1000 genomes]
rs2324344	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2324345	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs2324346	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2324347	0.81[CEU][hapmap]
rs3858867	0.81[CEU][hapmap]
rs4142372	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4456374	0.81[CEU][hapmap]
rs4567589	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5010893	0.83[EUR][1000 genomes]
rs7319551	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs927515	0.81[CEU][hapmap]
rs9315709	0.92[EUR][1000 genomes]
rs9548838	0.83[AMR][1000 genomes]
rs9566462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576869	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9576870	0.82[AMR][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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40140000-40169400	Weak transcription	Fetal Stomach	stomach
2	chr13:40140800-40165400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:40142000-40169400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr13:40142000-40169400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr13:40143200-40170800	Weak transcription	Osteobl	bone
6	chr13:40146000-40171800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:40150000-40172600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr13:40150400-40170600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr13:40150600-40171800	Weak transcription	HSMM	muscle
10	chr13:40153000-40171800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr13:40153200-40171800	Weak transcription	HMEC	breast
12	chr13:40153600-40170600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr13:40153600-40171800	Weak transcription	Aorta	Aorta
14	chr13:40155600-40170400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr13:40155600-40175800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:40156400-40171000	Weak transcription	Brain Hippocampus Middle	brain
17	chr13:40156400-40171000	Weak transcription	Brain Substantia Nigra	brain
18	chr13:40157000-40172000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:40158200-40165000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:40158200-40169400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:40158400-40169600	Weak transcription	Adipose Nuclei	Adipose
22	chr13:40158400-40171000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr13:40159200-40165000	Weak transcription	Colon Smooth Muscle	Colon
24	chr13:40159200-40170800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr13:40159400-40169400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr13:40161200-40175000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:40161600-40172000	Weak transcription	NHEK	skin
28	chr13:40161800-40166400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:40162400-40165400	Weak transcription	Right Atrium	heart
30	chr13:40162400-40165600	Weak transcription	Ovary	ovary
31	chr13:40162400-40165800	Weak transcription	Left Ventricle	heart
32	chr13:40162400-40169400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr13:40162400-40169400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr13:40162400-40169400	Weak transcription	Fetal Muscle Leg	muscle
35	chr13:40162400-40175000	Weak transcription	Lung	lung
36	chr13:40162400-40175000	Weak transcription	Spleen	Spleen
37	chr13:40162600-40169400	Weak transcription	Right Ventricle	heart
38	chr13:40163000-40171800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr13:40163200-40164800	Weak transcription	NHDF-Ad	bronchial
40	chr13:40163400-40175000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr13:40164400-40166000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr13:40164600-40165000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr13:40164600-40165000	Enhancers	Fetal Lung	lung
44	chr13:40164600-40165600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr13:40164600-40165800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr13:40164600-40165800	Enhancers	Fetal Heart	heart
47	chr13:40164600-40166000	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links