Variant report

Variant	rs9898500
Chromosome Location	chr17:38305381-38305382
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	GATA2	chr17:38305304-38305662	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr17:38305312-38305815	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38269477..38271026-chr17:38303126..38305486,2	MCF-7	breast:
2	chr17:38277369..38279890-chr17:38303923..38305640,2	MCF-7	breast:
3	chr17:38288588..38290508-chr17:38303480..38305638,2	MCF-7	breast:
4	chr17:38296494..38299896-chr17:38301046..38306469,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221555	TF binding region
ENSG00000108349	Chromatin interaction
ENSG00000188895	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10512482	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs1104761	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11540720	1.00[EUR][1000 genomes]
rs12103533	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs15685	0.92[EUR][1000 genomes]
rs16965660	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965669	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965734	1.00[EUR][1000 genomes]
rs16965736	1.00[EUR][1000 genomes]
rs16965748	1.00[EUR][1000 genomes]
rs16965774	1.00[EUR][1000 genomes]
rs16965778	1.00[EUR][1000 genomes]
rs17616543	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17616672	0.92[EUR][1000 genomes]
rs17616879	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17617263	0.92[EUR][1000 genomes]
rs17678817	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17678959	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17678990	0.92[EUR][1000 genomes]
rs17679086	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17679361	0.92[EUR][1000 genomes]
rs17680217	0.92[EUR][1000 genomes]
rs17680410	0.92[EUR][1000 genomes]
rs17680507	0.92[EUR][1000 genomes]
rs17680624	0.92[EUR][1000 genomes]
rs2012667	0.92[EUR][1000 genomes]
rs2229773	0.92[EUR][1000 genomes]
rs28362320	1.00[EUR][1000 genomes]
rs28362321	0.92[EUR][1000 genomes]
rs28526298	1.00[EUR][1000 genomes]
rs33998939	0.92[EUR][1000 genomes]
rs34270904	1.00[EUR][1000 genomes]
rs34300454	1.00[EUR][1000 genomes]
rs35783632	0.92[EUR][1000 genomes]
rs35898909	0.92[EUR][1000 genomes]
rs41283417	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41283423	0.92[EUR][1000 genomes]
rs4134993	0.92[EUR][1000 genomes]
rs4134998	0.92[EUR][1000 genomes]
rs4135005	0.92[EUR][1000 genomes]
rs4135007	0.92[EUR][1000 genomes]
rs4135012	0.92[EUR][1000 genomes]
rs4135019	0.92[EUR][1000 genomes]
rs4135021	0.92[EUR][1000 genomes]
rs4135027	0.92[EUR][1000 genomes]
rs4135030	0.92[EUR][1000 genomes]
rs45612441	0.92[EUR][1000 genomes]
rs8067519	1.00[EUR][1000 genomes]
rs8071687	1.00[EUR][1000 genomes]
rs8077482	1.00[EUR][1000 genomes]
rs9889905	0.85[EUR][1000 genomes]
rs9891944	0.92[EUR][1000 genomes]
rs9894364	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9894807	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9899425	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900154	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs9903261	0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs9903293	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9906274	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9909777	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9909811	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9910373	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915775	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9898500	RAPGEFL1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38297600-38306600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:38297600-38313400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:38297600-38318200	Weak transcription	Aorta	Aorta
4	chr17:38297600-38318200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:38297600-38325200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:38297800-38309400	Weak transcription	Right Ventricle	heart
7	chr17:38297800-38318400	Weak transcription	Stomach Mucosa	stomach
8	chr17:38297800-38333000	Strong transcription	Fetal Muscle Trunk	muscle
9	chr17:38297800-38336600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr17:38298000-38310800	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr17:38298000-38311800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr17:38298000-38324200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:38298000-38330400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:38298000-38330800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:38298200-38306200	Weak transcription	Fetal Brain Male	brain
16	chr17:38298200-38306400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr17:38298200-38307400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr17:38298200-38307600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr17:38298200-38308400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr17:38298200-38313000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr17:38298200-38313600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr17:38298200-38318000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr17:38298200-38318200	Weak transcription	Small Intestine	intestine
24	chr17:38298200-38324200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:38298200-38324400	Strong transcription	Fetal Stomach	stomach
26	chr17:38298200-38333000	Strong transcription	Fetal Thymus	thymus
27	chr17:38298400-38307000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:38298400-38324200	Weak transcription	Fetal Heart	heart
29	chr17:38298600-38307000	Strong transcription	Brain Anterior Caudate	brain
30	chr17:38298600-38309400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:38298600-38310600	Strong transcription	Lung	lung
32	chr17:38298600-38316400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr17:38298600-38319600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr17:38298600-38332200	Strong transcription	Fetal Intestine Small	intestine
35	chr17:38298800-38306400	Weak transcription	NHLF	lung
36	chr17:38298800-38313200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr17:38298800-38314000	Strong transcription	Fetal Muscle Leg	muscle
38	chr17:38299200-38319600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:38300000-38310200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr17:38300000-38312200	Strong transcription	Fetal Intestine Large	intestine
41	chr17:38300600-38306400	Weak transcription	Right Atrium	heart
42	chr17:38301400-38313400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr17:38301600-38307400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr17:38301600-38308400	Strong transcription	A549	lung
45	chr17:38301600-38324200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr17:38301800-38305400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:38301800-38305800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr17:38301800-38306000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr17:38301800-38306800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:38301800-38307600	Strong transcription	HSMM	muscle

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