Variant report

Variant	rs7224658
Chromosome Location	chr17:38485046-38485047
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	chr17:38135905..38138929-chr17:38484621..38486830,3	K562	blood:

Variant related genes	Relation type
ENSG00000108344	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];0.91[LWK][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12936565	1.00[ASW][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12937995	1.00[ASW][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12944531	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12947188	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34789145	1.00[ASW][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7213066	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7218938	0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8065665	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	0.85[LWK][hapmap];0.87[MKK][hapmap]
rs8067148	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8072718	0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8074251	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8076915	1.00[ASW][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9892367	0.92[ASW][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap];0.84[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
rs7224658	RAPGEFL1	cis	lymphoblastoid	seeQTL
rs7224658	RAPGEFL1	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 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	chr17:38479200-38494400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr17:38479400-38486600	Weak transcription	Fetal Brain Male	brain
4	chr17:38479400-38489600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr17:38479400-38491600	Enhancers	Fetal Heart	heart
6	chr17:38479600-38485400	Enhancers	Right Ventricle	heart
7	chr17:38479600-38487600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:38479600-38490200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr17:38479600-38491200	Weak transcription	Fetal Kidney	kidney
10	chr17:38479800-38488200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr17:38480000-38486600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr17:38480000-38487000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:38480000-38487200	Enhancers	Fetal Thymus	thymus
14	chr17:38480000-38487600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:38480400-38486200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr17:38480400-38487200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:38480400-38487400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:38480800-38485400	Enhancers	Thymus	Thymus
19	chr17:38480800-38485600	Enhancers	Colon Smooth Muscle	Colon
20	chr17:38480800-38487400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:38481000-38486200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr17:38481600-38487200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr17:38482600-38486200	Weak transcription	Brain Angular Gyrus	brain
24	chr17:38482800-38486200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr17:38483000-38486200	Enhancers	Primary B cells from peripheral blood	blood
26	chr17:38483200-38485400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:38483200-38486200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:38483200-38486200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:38483200-38486200	Weak transcription	Dnd41	blood
30	chr17:38483200-38486200	Weak transcription	HMEC	breast
31	chr17:38483200-38486200	Weak transcription	HUVEC	blood vessel
32	chr17:38483200-38487400	Weak transcription	Aorta	Aorta
33	chr17:38483400-38485200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr17:38483400-38486200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:38483400-38486200	Weak transcription	Hela-S3	cervix
36	chr17:38483400-38486600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr17:38483400-38490800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:38483600-38485200	Enhancers	Rectal Smooth Muscle	rectum
39	chr17:38483600-38486200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr17:38483600-38486200	Weak transcription	NH-A	brain
41	chr17:38483800-38485200	Enhancers	NHEK	skin
42	chr17:38483800-38486000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:38483800-38486200	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr17:38484000-38485200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:38484000-38486200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr17:38484000-38486200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr17:38484000-38486200	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr17:38484000-38486200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr17:38484000-38486200	Enhancers	A549	lung
50	chr17:38484000-38486400	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links