Variant report

Variant	rs12937995
Chromosome Location	chr17:38468090-38468091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38467928..38470540-chr17:39686784..39688298,2	MCF-7	breast:
2	chr17:38467242..38468163-chr17:38478272..38479147,4	MCF-7	breast:
3	chr17:38467259..38468169-chr17:38478282..38479199,16	MCF-7	breast:
4	chr17:38468056..38470657-chr17:39666914..39669365,2	MCF-7	breast:
5	chr17:38467638..38468555-chr17:38604606..38605466,3	MCF-7	breast:
6	chr17:38467971..38471563-chr17:39690230..39693084,3	MCF-7	breast:
7	chr17:38466898..38469378-chr17:39682099..39684808,2	MCF-7	breast:
8	chr17:38467277..38468555-chr17:38604606..38605531,7	MCF-7	breast:
9	chr17:38467163..38469304-chr17:38482275..38484849,2	K562	blood:
10	chr17:38467259..38468192-chr17:38478282..38479199,12	MCF-7	breast:
11	chr17:38331368..38338782-chr17:38460574..38470405,11	MCF-7	breast:
12	chr17:38461615..38484404-chr17:38597525..38608992,85	MCF-7	breast:
13	chr17:38467078..38468947-chr17:38685265..38686979,2	MCF-7	breast:
14	chr17:38464338..38472007-chr17:38495904..38503617,17	K562	blood:

No data

Variant related genes	Relation type
ENSG00000131759	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000171345	Chromatin interaction
ENSG00000141753	Chromatin interaction
ENSG00000265666	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1130199	0.92[ASW][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11651042	1.00[CEU][hapmap]
rs11867497	1.00[MEX][hapmap]
rs12936565	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12944531	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12947188	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28742572	1.00[MEX][hapmap]
rs34530029	1.00[MEX][hapmap]
rs34789145	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35487582	1.00[CEU][hapmap]
rs4135013	1.00[CEU][hapmap]
rs4135034	1.00[MEX][hapmap]
rs7213066	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7218938	0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7224658	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]
rs8065665	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]
rs8066144	0.85[LWK][hapmap];0.91[MKK][hapmap]
rs8067148	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8072718	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8074251	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8076915	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9892367	0.92[ASW][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9913992	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1825614	chr17:38466377-38481100	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12937995	RAPGEFL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38459200-38473800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr17:38462200-38473200	Enhancers	NHDF-Ad	bronchial
3	chr17:38462400-38468800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:38462600-38468200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr17:38462600-38469800	Flanking Active TSS	Hela-S3	cervix
6	chr17:38462600-38474000	Enhancers	Lung	lung
7	chr17:38462800-38473000	Enhancers	Psoas Muscle	Psoas
8	chr17:38463000-38469600	Enhancers	Small Intestine	intestine
9	chr17:38465000-38469400	Flanking Active TSS	GM12878-XiMat	blood
10	chr17:38465200-38469800	Flanking Active TSS	Fetal Heart	heart
11	chr17:38465600-38473200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:38465800-38468600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr17:38465800-38469000	Enhancers	Ovary	ovary
14	chr17:38465800-38472800	Enhancers	Esophagus	oesophagus
15	chr17:38465800-38473000	Enhancers	Placenta	Placenta
16	chr17:38465800-38473000	Enhancers	Right Ventricle	heart
17	chr17:38465800-38473400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr17:38465800-38473800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr17:38465800-38474000	Enhancers	Spleen	Spleen
20	chr17:38466000-38468800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:38466000-38469400	Enhancers	Primary B cells from peripheral blood	blood
22	chr17:38466000-38469800	Enhancers	Primary B cells from cord blood	blood
23	chr17:38466000-38471200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:38466000-38471800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:38466000-38471800	Enhancers	Gastric	stomach
26	chr17:38466000-38472400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:38466000-38472600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:38466000-38472600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr17:38466000-38472600	Enhancers	HMEC	breast
30	chr17:38466000-38473000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:38466000-38473000	Enhancers	Left Ventricle	heart
32	chr17:38466000-38473800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr17:38466200-38468600	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr17:38466200-38469200	Enhancers	Brain Cingulate Gyrus	brain
35	chr17:38466200-38471400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:38466200-38471400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr17:38466200-38471400	Enhancers	Liver	Liver
38	chr17:38466200-38471600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr17:38466200-38471800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr17:38466200-38471800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr17:38466200-38472000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:38466200-38472200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr17:38466200-38472600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr17:38466200-38473000	Enhancers	Fetal Muscle Leg	muscle
45	chr17:38466200-38473400	Enhancers	Pancreas	Pancrea
46	chr17:38466200-38473600	Enhancers	Primary hematopoietic stem cells	blood
47	chr17:38466200-38473800	Enhancers	Fetal Thymus	thymus
48	chr17:38466400-38468200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr17:38466400-38468600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr17:38466400-38468600	Enhancers	HSMMtube	muscle

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