Variant report

Variant	rs475009
Chromosome Location	chr1:93466402-93466403
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93300622..93302663-chr1:93466102..93468590,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122406	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1011663	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11164855	0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4847226	0.90[EUR][1000 genomes]
rs557095	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs579800	0.91[ASN][1000 genomes]
rs655026	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs475009	FAM69A	cis	Thyroid	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93463800-93467600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:93465200-93468000	Enhancers	Fetal Intestine Small	intestine
3	chr1:93465600-93467200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:93465800-93466600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:93465800-93466800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:93465800-93467000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr1:93465800-93467000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:93465800-93467000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:93465800-93467000	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:93465800-93467000	Enhancers	Brain Substantia Nigra	brain
11	chr1:93465800-93467200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:93465800-93467200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:93466000-93466600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:93466000-93466600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:93466000-93466600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:93466000-93466600	Enhancers	Ovary	ovary
17	chr1:93466000-93466600	Enhancers	Pancreas	Pancrea
18	chr1:93466000-93466600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:93466000-93466600	Enhancers	Small Intestine	intestine
20	chr1:93466000-93466800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:93466000-93466800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:93466000-93466800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:93466000-93466800	Enhancers	Brain Germinal Matrix	brain
24	chr1:93466000-93466800	Enhancers	Fetal Stomach	stomach
25	chr1:93466000-93466800	Enhancers	HMEC	breast
26	chr1:93466000-93466800	Enhancers	HSMM	muscle
27	chr1:93466000-93467000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:93466000-93467000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:93466000-93467000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:93466000-93467000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:93466000-93467000	Enhancers	Brain Angular Gyrus	brain
32	chr1:93466000-93467000	Enhancers	Brain Anterior Caudate	brain
33	chr1:93466000-93467000	Enhancers	Brain Hippocampus Middle	brain
34	chr1:93466000-93467000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr1:93466000-93467000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr1:93466000-93467000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:93466000-93467000	Bivalent Enhancer	NH-A	brain
38	chr1:93466000-93467000	Enhancers	NHEK	skin
39	chr1:93466000-93467200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:93466000-93467200	Enhancers	Fetal Lung	lung
41	chr1:93466000-93467400	Enhancers	Fetal Muscle Leg	muscle
42	chr1:93466000-93468000	Enhancers	Fetal Intestine Large	intestine
43	chr1:93466200-93466800	Enhancers	Colon Smooth Muscle	Colon
44	chr1:93466200-93466800	Weak transcription	Placenta	Placenta
45	chr1:93466200-93466800	Enhancers	Osteobl	bone
46	chr1:93466200-93467000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:93466200-93467200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
48	chr1:93466400-93466600	Flanking Active TSS	GM12878-XiMat	blood
49	chr1:93466400-93466600	Flanking Active TSS	HSMMtube	muscle
50	chr1:93466400-93467000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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