Variant report

Variant	rs9911936
Chromosome Location	chr17:38333032-38333033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38332285-38334132	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr17:38332675-38334179	U87	brain:	n/a	n/a
3	POLR2A	chr17:38332716-38333228	MCF-7	breast:	n/a	n/a
4	MAX	chr17:38332471-38334154	ECC-1	luminal epithelium:	n/a	chr17:38334103-38334113 chr17:38333694-38333704 chr17:38332900-38332910 chr17:38333797-38333807 chr17:38333082-38333091
5	POLR2A	chr17:38332705-38334026	Hela-S3	cervix:	n/a	n/a
6	MAX	chr17:38332540-38334179	ECC-1	luminal epithelium:	n/a	chr17:38334103-38334113 chr17:38333694-38333704 chr17:38332900-38332910 chr17:38333797-38333807 chr17:38333082-38333091
7	POLR2A	chr17:38333009-38333377	H1-hESC	embryonic stem cell:	n/a	n/a
8	RFX5	chr17:38332944-38333221	Hela-S3	cervix:	n/a	n/a
9	MYC	chr17:38332502-38333362	MCF10A-Er-Src	breast:	n/a	chr17:38332900-38332910 chr17:38333082-38333091
10	POLR2A	chr17:38332825-38333176	H1-hESC	embryonic stem cell:	n/a	n/a
11	MYC	chr17:38332487-38333800	MCF10A-Er-Src	breast:	n/a	chr17:38333694-38333704 chr17:38332900-38332910 chr17:38333082-38333091
12	POLR2A	chr17:38332637-38333485	HepG2	liver:	n/a	n/a
13	POLR2A	chr17:38332657-38333922	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr17:38332995-38333367	K562	blood:	n/a	n/a
15	RFX5	chr17:38332988-38333070	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38274376..38281367-chr17:38331383..38338006,23	MCF-7	breast:
2	chr17:38331383..38339312-chr17:38470464..38480799,28	MCF-7	breast:
3	chr17:38330070..38334400-chr17:38346938..38351108,4	K562	blood:
4	chr17:38276815..38279338-chr17:38332365..38335401,3	MCF-7	breast:
5	chr17:38177907..38180041-chr17:38332919..38334626,2	MCF-7	breast:
6	chr17:38331368..38338782-chr17:38460574..38470405,11	MCF-7	breast:
7	chr17:38331593..38335002-chr17:38443466..38446781,3	MCF-7	breast:

Variant related genes	Relation type
RAPGEFL1	TF binding region
ENSG00000108352	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000094804	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2227334	1.00[MEX][hapmap]
rs28410661	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28750099	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7206995	1.00[ASW][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7218663	1.00[MEX][hapmap]
rs7501734	1.00[MEX][hapmap]
rs8082130	1.00[MEX][hapmap]
rs9890792	1.00[MEX][hapmap]
rs9896339	0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9898129	1.00[MEX][hapmap]
rs9903261	0.91[ASW][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap]
rs9904120	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9906274	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs9909548	0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9910546	0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9911936	RAPGEFL1	cis	lymphoblastoid	seeQTL
rs9911936	RAPGEFL1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38297800-38336600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:38308200-38333200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr17:38314800-38333200	Weak transcription	Right Atrium	heart
4	chr17:38316200-38333200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:38317200-38333200	Strong transcription	Thymus	Thymus
6	chr17:38317400-38333400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr17:38317400-38333800	Strong transcription	Dnd41	blood
8	chr17:38317600-38333200	Strong transcription	Left Ventricle	heart
9	chr17:38322400-38333200	Weak transcription	Psoas Muscle	Psoas
10	chr17:38324800-38333200	Strong transcription	Adipose Nuclei	Adipose
11	chr17:38327000-38336600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:38328200-38333400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:38328400-38333200	Weak transcription	Small Intestine	intestine
14	chr17:38328600-38333200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:38328600-38333400	Weak transcription	NH-A	brain
16	chr17:38328800-38333200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr17:38328800-38333200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr17:38328800-38333200	Weak transcription	Fetal Kidney	kidney
19	chr17:38329000-38333200	Weak transcription	HUVEC	blood vessel
20	chr17:38330000-38333200	Weak transcription	Primary B cells from cord blood	blood
21	chr17:38330000-38333200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr17:38330000-38333200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:38330000-38333200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr17:38330000-38333200	Weak transcription	Ovary	ovary
25	chr17:38330000-38333200	Weak transcription	NHDF-Ad	bronchial
26	chr17:38330000-38333400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr17:38330400-38333200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:38330400-38333200	Weak transcription	GM12878-XiMat	blood
29	chr17:38330600-38333200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr17:38331000-38333400	Strong transcription	HepG2	liver
31	chr17:38331200-38333200	Weak transcription	Colon Smooth Muscle	Colon
32	chr17:38331200-38333200	Weak transcription	HSMMtube	muscle
33	chr17:38331400-38333200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr17:38331400-38333200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr17:38331400-38333200	Weak transcription	Brain Germinal Matrix	brain
36	chr17:38331400-38333200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr17:38331400-38333200	Weak transcription	Osteobl	bone
38	chr17:38331400-38333400	Weak transcription	Primary T cells from cord blood	blood
39	chr17:38331400-38333800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr17:38331400-38338200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr17:38331800-38333200	Strong transcription	NHLF	lung
42	chr17:38332000-38333200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr17:38332000-38333200	Enhancers	Esophagus	oesophagus
44	chr17:38332200-38333200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
45	chr17:38332200-38333200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr17:38332200-38333400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
47	chr17:38332200-38333600	Genic enhancers	Fetal Intestine Small	intestine
48	chr17:38332200-38333600	Genic enhancers	A549	lung
49	chr17:38332200-38333800	Enhancers	Fetal Intestine Large	intestine
50	chr17:38332400-38333200	Active TSS	Rectal Smooth Muscle	rectum

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