Variant report

Variant	rs899604
Chromosome Location	chr14:56711146-56711147
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	chr14:56711133..56713005-chr14:56715491..56717445,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10150333	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11158082	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1117310	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1382973	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs173352	0.83[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap]
rs2054491	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054492	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2086326	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs242578	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs242583	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs242590	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs242591	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3783675	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3844020	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs3912201	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4143949	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7140444	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7145330	0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7151741	0.91[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1844788	chr14:56594420-56771207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1044886	chr14:56689682-56834648	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv542104	chr14:56689682-56834648	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs899604	GCH1	cis	cerebellum	SCAN
rs899604	MAPK1IP1L	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56689800-56715800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr14:56693200-56724400	Weak transcription	Gastric	stomach
3	chr14:56694000-56723000	Weak transcription	Lung	lung
4	chr14:56696000-56715600	Weak transcription	Fetal Thymus	thymus
5	chr14:56702600-56717600	Weak transcription	Ovary	ovary
6	chr14:56704000-56716800	Weak transcription	Fetal Intestine Small	intestine
7	chr14:56704400-56716600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr14:56704600-56715200	Weak transcription	Aorta	Aorta
9	chr14:56704600-56716000	Weak transcription	Primary T cells from cord blood	blood
10	chr14:56707200-56717400	Weak transcription	Pancreas	Pancrea
11	chr14:56707400-56715200	Weak transcription	Thymus	Thymus
12	chr14:56707600-56716200	Weak transcription	Primary B cells from cord blood	blood
13	chr14:56708400-56711200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:56708800-56711200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr14:56709000-56714800	Weak transcription	Dnd41	blood
16	chr14:56710000-56711400	Enhancers	Fetal Stomach	stomach
17	chr14:56710000-56711400	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr14:56710000-56711600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr14:56710000-56712000	Enhancers	NHLF	lung
20	chr14:56710600-56711200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr14:56710600-56711200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr14:56710600-56711200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr14:56710600-56711600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr14:56710600-56711600	Enhancers	Colon Smooth Muscle	Colon
25	chr14:56710600-56711600	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr14:56710600-56711600	Flanking Active TSS	NHDF-Ad	bronchial
27	chr14:56710600-56717200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr14:56710800-56711200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr14:56710800-56711200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr14:56710800-56711200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr14:56710800-56711200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:56710800-56711200	Enhancers	HSMMtube	muscle
33	chr14:56710800-56711400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr14:56710800-56711400	Flanking Active TSS	A549	lung
35	chr14:56710800-56711400	Enhancers	HSMM	muscle
36	chr14:56710800-56711600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr14:56710800-56711600	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr14:56710800-56711600	Flanking Active TSS	NH-A	brain
39	chr14:56710800-56711800	Flanking Active TSS	Osteobl	bone
40	chr14:56711000-56711200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr14:56711000-56711400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:56711000-56711600	Enhancers	Fetal Brain Male	brain

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