Variant report

Variant	rs4925094
Chromosome Location	chr17:17569012-17569013
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17566953..17570560-chr17:17583425..17585790,3	K562	blood:
2	chr17:17566041..17569411-chr17:17596920..17599764,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108557	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12940014	0.89[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2001884	0.81[CEU][hapmap]
rs2350632	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4496218	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924807	0.85[EUR][1000 genomes]
rs4925092	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4925093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925095	0.85[EUR][1000 genomes]
rs4925096	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4925102	0.87[EUR][1000 genomes]
rs4925104	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4925105	0.89[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6502613	0.89[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs6502615	0.85[CEU][hapmap]
rs7208561	0.82[CEU][hapmap]
rs7214245	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7224617	0.89[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs7224619	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7224739	0.82[CEU][hapmap]
rs7225141	0.84[MEX][hapmap]
rs7225934	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065154	0.85[CEU][hapmap]
rs8075153	0.85[CEU][hapmap]
rs897457	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897044	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9897309	0.89[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs9897596	0.86[EUR][1000 genomes]
rs9899364	0.80[AMR][1000 genomes]
rs9904468	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9906532	0.82[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4925094	SREBF1	cis	cerebellum	SCAN
rs4925094	TOM1L2	cis	parietal	SCAN
rs4925094	FAM106A	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17566400-17570200	Enhancers	Fetal Stomach	stomach
2	chr17:17566600-17572200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr17:17567000-17570400	Weak transcription	Pancreas	Pancrea
4	chr17:17567000-17572200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr17:17567000-17572200	Weak transcription	Fetal Brain Female	brain
6	chr17:17567000-17572200	Weak transcription	Fetal Heart	heart
7	chr17:17567000-17572200	Weak transcription	Gastric	stomach
8	chr17:17567000-17572400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr17:17567000-17573200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:17567200-17569400	Weak transcription	Esophagus	oesophagus
11	chr17:17567200-17569400	Weak transcription	A549	lung
12	chr17:17567200-17569400	Weak transcription	NHLF	lung
13	chr17:17567200-17569800	Weak transcription	Colonic Mucosa	Colon
14	chr17:17567200-17571000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr17:17567200-17572200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:17567200-17572200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:17567200-17572200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr17:17567200-17572400	Weak transcription	Fetal Brain Male	brain
19	chr17:17567200-17572600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr17:17567200-17572600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr17:17567200-17574400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr17:17567200-17575400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr17:17567200-17579200	Weak transcription	K562	blood
24	chr17:17567400-17569400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:17567400-17569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:17567400-17569400	Weak transcription	HMEC	breast
27	chr17:17567400-17569400	Weak transcription	HSMM	muscle
28	chr17:17567400-17569600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr17:17567400-17569600	Weak transcription	HSMMtube	muscle
30	chr17:17567400-17572400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:17567400-17575400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr17:17567600-17569400	Weak transcription	NH-A	brain
33	chr17:17568000-17569400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr17:17568000-17569800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr17:17568200-17571400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:17568200-17573800	Weak transcription	Left Ventricle	heart
37	chr17:17568200-17576200	Weak transcription	Spleen	Spleen
38	chr17:17568600-17570000	Enhancers	Fetal Muscle Leg	muscle
39	chr17:17568800-17569400	Bivalent Enhancer	HepG2	liver
40	chr17:17568800-17569600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr17:17568800-17570000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr17:17568800-17571800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:17568800-17572000	Enhancers	NHEK	skin
44	chr17:17568800-17574000	Enhancers	Fetal Thymus	thymus
45	chr17:17569000-17569400	Weak transcription	Thymus	Thymus
46	chr17:17569000-17575600	Weak transcription	GM12878-XiMat	blood

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