Variant report

Variant	rs9898129
Chromosome Location	chr17:38265949-38265950
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38263117..38266703-chr17:38295355..38298359,3	K562	blood:
2	chr17:38136352..38138550-chr17:38264781..38266286,2	K562	blood:
3	chr17:38170125..38172136-chr17:38264853..38266988,2	K562	blood:
4	chr17:38264983..38267583-chr17:38284257..38287592,3	MCF-7	breast:
5	chr17:38191328..38192049-chr17:38265556..38266184,3	MCF-7	breast:
6	chr17:38264485..38267418-chr17:38331477..38333568,2	K562	blood:
7	chr17:38241415..38245258-chr17:38262802..38266509,3	K562	blood:

Variant related genes	Relation type
ENSG00000108349	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000108342	Chromatin interaction
ENSG00000265799	Chromatin interaction
ENSG00000108344	Chromatin interaction
ENSG00000108352	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16965644	0.81[ASW][hapmap]
rs2227334	1.00[MEX][hapmap]
rs41365448	1.00[MEX][hapmap]
rs7501734	1.00[MEX][hapmap]
rs8077482	0.89[AFR][1000 genomes]
rs8082130	1.00[MEX][hapmap]
rs9890792	1.00[MEX][hapmap]
rs9894164	1.00[MEX][hapmap]
rs9903261	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs9910635	1.00[MEX][hapmap]
rs9911936	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv908221	chr17:38216522-38289003	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	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
3	nsv528369	chr17:38256693-38289003	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9898129	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	chr17:38256800-38269800	Weak transcription	Aorta	Aorta
2	chr17:38257400-38267200	Enhancers	Fetal Muscle Trunk	muscle
3	chr17:38257400-38267200	Enhancers	Fetal Muscle Leg	muscle
4	chr17:38257400-38267400	Enhancers	Fetal Intestine Small	intestine
5	chr17:38257400-38267800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr17:38257400-38269600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:38257400-38269600	Enhancers	Fetal Thymus	thymus
8	chr17:38257600-38267200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:38257600-38267400	Enhancers	Primary T cells from cord blood	blood
10	chr17:38257600-38267600	Enhancers	Primary T cells fromperipheralblood	blood
11	chr17:38257600-38269600	Enhancers	Fetal Intestine Large	intestine
12	chr17:38257600-38269600	Enhancers	Placenta	Placenta
13	chr17:38257800-38266000	Enhancers	Stomach Mucosa	stomach
14	chr17:38259000-38266000	Enhancers	Esophagus	oesophagus
15	chr17:38259000-38267400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:38259000-38267600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr17:38259000-38267600	Enhancers	HSMM	muscle
18	chr17:38259000-38269600	Enhancers	Fetal Stomach	stomach
19	chr17:38259200-38266000	Enhancers	Lung	lung
20	chr17:38259400-38269600	Enhancers	Primary hematopoietic stem cells	blood
21	chr17:38259800-38267400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:38260800-38269600	Enhancers	Left Ventricle	heart
23	chr17:38261000-38267400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr17:38261000-38267400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr17:38261800-38266000	Weak transcription	Hela-S3	cervix
26	chr17:38261800-38269600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr17:38262000-38267800	Enhancers	Small Intestine	intestine
28	chr17:38262200-38270400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr17:38262400-38267200	Enhancers	NHLF	lung
30	chr17:38262800-38267800	Enhancers	Primary B cells from cord blood	blood
31	chr17:38263200-38266200	Weak transcription	Ovary	ovary
32	chr17:38263200-38267000	Enhancers	HUVEC	blood vessel
33	chr17:38263200-38267600	Weak transcription	Gastric	stomach
34	chr17:38263200-38267800	Enhancers	Duodenum Mucosa	Duodenum
35	chr17:38263400-38267400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr17:38263400-38272400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:38263600-38267400	Enhancers	A549	lung
38	chr17:38263600-38267800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr17:38263800-38267600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr17:38263800-38267600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr17:38264000-38267200	Enhancers	Fetal Lung	lung
42	chr17:38264000-38270400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:38264200-38266200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr17:38264200-38267200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr17:38264200-38267400	Enhancers	Colonic Mucosa	Colon
46	chr17:38264200-38267600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr17:38264400-38266000	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr17:38264400-38266200	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr17:38264400-38267000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:38264400-38267400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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