Variant report

Variant	rs8065665
Chromosome Location	chr17:38482263-38482264
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38481232..38483242-chr17:38705290..38708203,2	MCF-7	breast:
2	chr17:38480856..38482553-chr21:29598509..29601489,2	MCF-7	breast:
3	chr17:38481166..38483354-chr17:38771299..38774149,2	MCF-7	breast:
4	chr17:38479395..38482301-chr17:38490961..38492662,2	K562	blood:
5	chr17:38480192..38482412-chr17:38766976..38769922,2	MCF-7	breast:
6	chr17:38461615..38484404-chr17:38597525..38608992,85	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236532	Chromatin interaction
ENSG00000141753	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1130199	0.92[ASW][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12936565	1.00[ASW][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12937995	1.00[ASW][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12944531	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12947188	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34789145	1.00[ASW][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7213066	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7218938	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7224658	1.00[ASW][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8066144	0.82[LWK][hapmap];0.83[MKK][hapmap]
rs8067148	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8072718	0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8074251	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8076915	1.00[ASW][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9892367	0.92[ASW][hapmap];0.88[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058194	chr17:38457226-38502453	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1063310	chr17:38467043-38499351	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv1057471	chr17:38467043-38502453	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1058540	chr17:38467043-38515087	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8065665	RAPGEFL1	cis	multi-tissue	Pritchard
rs8065665	RAPGEFL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38474800-38487000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr17:38475600-38482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:38475600-38484600	Enhancers	Placenta	Placenta
4	chr17:38475600-38484600	Enhancers	Spleen	Spleen
5	chr17:38475600-38484800	Enhancers	Stomach Mucosa	stomach
6	chr17:38476200-38485000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr17:38477600-38484800	Enhancers	Ovary	ovary
8	chr17:38478400-38483200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:38478600-38482600	Weak transcription	Aorta	Aorta
10	chr17:38478800-38483400	Enhancers	Hela-S3	cervix
11	chr17:38478800-38484600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr17:38478800-38484600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr17:38478800-38484600	Enhancers	Small Intestine	intestine
14	chr17:38479000-38482800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr17:38479000-38483800	Genic enhancers	Fetal Stomach	stomach
16	chr17:38479000-38484200	Genic enhancers	Fetal Intestine Small	intestine
17	chr17:38479000-38484600	Enhancers	Lung	lung
18	chr17:38479000-38485000	Enhancers	Psoas Muscle	Psoas
19	chr17:38479200-38482600	Enhancers	Liver	Liver
20	chr17:38479200-38484200	Enhancers	Fetal Intestine Large	intestine
21	chr17:38479200-38494400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr17:38479400-38484600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr17:38479400-38484600	Enhancers	Left Ventricle	heart
24	chr17:38479400-38485000	Enhancers	NHDF-Ad	bronchial
25	chr17:38479400-38486600	Weak transcription	Fetal Brain Male	brain
26	chr17:38479400-38489600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr17:38479400-38491600	Enhancers	Fetal Heart	heart
28	chr17:38479600-38482800	Enhancers	A549	lung
29	chr17:38479600-38484400	Enhancers	HSMMtube	muscle
30	chr17:38479600-38485000	Enhancers	Fetal Lung	lung
31	chr17:38479600-38485000	Enhancers	Right Atrium	heart
32	chr17:38479600-38485400	Enhancers	Right Ventricle	heart
33	chr17:38479600-38487600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:38479600-38490200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr17:38479600-38491200	Weak transcription	Fetal Kidney	kidney
36	chr17:38479800-38482400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr17:38479800-38482600	Enhancers	Fetal Muscle Trunk	muscle
38	chr17:38479800-38483200	Enhancers	HUVEC	blood vessel
39	chr17:38479800-38485000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:38479800-38488200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr17:38480000-38482400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr17:38480000-38483800	Enhancers	NHLF	lung
43	chr17:38480000-38486600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr17:38480000-38487000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr17:38480000-38487200	Enhancers	Fetal Thymus	thymus
46	chr17:38480000-38487600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr17:38480400-38482800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr17:38480400-38482800	Enhancers	HepG2	liver
49	chr17:38480400-38484600	Enhancers	Primary hematopoietic stem cells	blood
50	chr17:38480400-38484600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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