Variant report

Variant	rs7225141
Chromosome Location	chr17:17570827-17570828
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	chr17:17569394..17571132-chr17:17584796..17587607,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108557	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12449524	0.83[ASW][hapmap]
rs2001421	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2350962	0.88[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs4636969	0.86[EUR][1000 genomes]
rs4925062	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925093	0.84[MEX][hapmap]
rs4925094	0.84[MEX][hapmap]
rs4995264	0.88[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7209595	0.84[CEU][hapmap]
rs8067800	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9783803	0.91[ASN][1000 genomes]
rs9899364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9900148	0.86[EUR][1000 genomes]
rs9905702	0.84[CEU][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs9905728	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv869118	chr17:17509896-17599850	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv907751	chr17:17530554-17581184	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv907752	chr17:17569012-17750907	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7225141	TOM1L2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17566600-17572200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr17:17567000-17572200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr17:17567000-17572200	Weak transcription	Fetal Brain Female	brain
4	chr17:17567000-17572200	Weak transcription	Fetal Heart	heart
5	chr17:17567000-17572200	Weak transcription	Gastric	stomach
6	chr17:17567000-17572400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr17:17567000-17573200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:17567200-17571000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:17567200-17572200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:17567200-17572200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:17567200-17572200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr17:17567200-17572400	Weak transcription	Fetal Brain Male	brain
13	chr17:17567200-17572600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr17:17567200-17572600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr17:17567200-17574400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr17:17567200-17575400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr17:17567200-17579200	Weak transcription	K562	blood
18	chr17:17567400-17572400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:17567400-17575400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr17:17568200-17571400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:17568200-17573800	Weak transcription	Left Ventricle	heart
22	chr17:17568200-17576200	Weak transcription	Spleen	Spleen
23	chr17:17568800-17571800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:17568800-17572000	Enhancers	NHEK	skin
25	chr17:17568800-17574000	Enhancers	Fetal Thymus	thymus
26	chr17:17569000-17575600	Weak transcription	GM12878-XiMat	blood
27	chr17:17569400-17572600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:17569400-17572800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr17:17569400-17572800	Enhancers	HMEC	breast
30	chr17:17569600-17571600	Weak transcription	Thymus	Thymus
31	chr17:17570000-17571200	Weak transcription	Fetal Muscle Leg	muscle
32	chr17:17570000-17572200	Weak transcription	NH-A	brain
33	chr17:17570000-17576000	Weak transcription	Right Ventricle	heart
34	chr17:17570200-17571200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:17570200-17571600	Weak transcription	Colonic Mucosa	Colon
36	chr17:17570200-17572200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr17:17570200-17575600	Weak transcription	Hela-S3	cervix
38	chr17:17570400-17572000	Weak transcription	HSMMtube	muscle
39	chr17:17570600-17571000	Enhancers	Liver	Liver
40	chr17:17570600-17571400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:17570600-17572000	Weak transcription	HSMM	muscle
42	chr17:17570800-17571600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr17:17570800-17572600	Weak transcription	Pancreas	Pancrea
44	chr17:17570800-17572600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr17:17570800-17574000	Enhancers	HepG2	liver
46	chr17:17570800-17574600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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