Variant report

Variant	rs9900154
Chromosome Location	chr17:38283199-38283200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38194560..38196821-chr17:38283117..38285170,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10512482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1104761	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11540720	1.00[EUR][1000 genomes]
rs12103533	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs15685	0.92[EUR][1000 genomes]
rs16965660	1.00[CEU][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965734	1.00[EUR][1000 genomes]
rs16965736	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]
rs2229773	0.92[EUR][1000 genomes]
rs28526298	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];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	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	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9894807	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9898500	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs9899425	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9903261	0.82[YRI][hapmap]
rs9903293	1.00[EUR][1000 genomes]
rs9906274	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9909777	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9909811	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9910373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915775	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]

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
rs9900154	RAPGEFL1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38281000-38283400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:38281000-38285600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:38281200-38283200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr17:38281200-38283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:38281200-38285000	Weak transcription	Colonic Mucosa	Colon
6	chr17:38281200-38285600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:38281200-38293800	Strong transcription	Fetal Muscle Leg	muscle
8	chr17:38281200-38294800	Strong transcription	Fetal Thymus	thymus
9	chr17:38281200-38295800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr17:38281400-38283800	Strong transcription	K562	blood
11	chr17:38281400-38286400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr17:38281400-38293800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:38281400-38294600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:38281400-38294800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:38281400-38295600	Weak transcription	Right Atrium	heart
16	chr17:38281600-38285600	Strong transcription	A549	lung
17	chr17:38281600-38289200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr17:38281600-38294200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:38281800-38283400	Weak transcription	HSMMtube	muscle
20	chr17:38281800-38285200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr17:38281800-38289200	Strong transcription	Fetal Intestine Small	intestine
22	chr17:38281800-38292200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr17:38281800-38293800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:38281800-38293800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr17:38281800-38294000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr17:38281800-38294000	Strong transcription	NHEK	skin
27	chr17:38281800-38294200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr17:38281800-38294200	Strong transcription	HMEC	breast
29	chr17:38281800-38294400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:38281800-38294800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:38281800-38295000	Strong transcription	Fetal Stomach	stomach
32	chr17:38282000-38284000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:38282000-38284000	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr17:38282000-38284200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr17:38282000-38284400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr17:38282000-38285200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr17:38282000-38286600	Strong transcription	Fetal Intestine Large	intestine
38	chr17:38282000-38286600	Strong transcription	Placenta	Placenta
39	chr17:38282000-38289800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr17:38282000-38291200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:38282000-38292200	Strong transcription	Lung	lung
42	chr17:38282000-38293600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr17:38282000-38293600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr17:38282000-38293600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr17:38282000-38293600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr17:38282000-38293600	Strong transcription	Liver	Liver
47	chr17:38282000-38293800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr17:38282000-38294000	Strong transcription	Thymus	Thymus
49	chr17:38282000-38294200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr17:38282000-38294200	Strong transcription	Fetal Lung	lung

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