Variant report

Variant	rs9909777
Chromosome Location	chr17:38308343-38308344
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	chr17:38301912..38303464-chr17:38307519..38309696,2	K562	blood:
2	chr17:38301964..38305074-chr17:38307464..38309696,4	K562	blood:

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

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10512482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap];0.90[AFR][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];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs15685	0.92[EUR][1000 genomes]
rs16965660	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16965669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.83[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	0.92[AFR][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	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8071687	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8077482	1.00[EUR][1000 genomes]
rs9889905	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9891944	0.92[EUR][1000 genomes]
rs9894364	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9894807	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9898500	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9899425	1.00[EUR][1000 genomes]
rs9900154	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]
rs9903293	1.00[EUR][1000 genomes]
rs9906274	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9909811	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.83[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];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915775	1.00[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9909777	RAPGEFL1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38297600-38313400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:38297600-38318200	Weak transcription	Aorta	Aorta
3	chr17:38297600-38318200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:38297600-38325200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:38297800-38309400	Weak transcription	Right Ventricle	heart
6	chr17:38297800-38318400	Weak transcription	Stomach Mucosa	stomach
7	chr17:38297800-38333000	Strong transcription	Fetal Muscle Trunk	muscle
8	chr17:38297800-38336600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr17:38298000-38310800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr17:38298000-38311800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:38298000-38324200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:38298000-38330400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr17:38298000-38330800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:38298200-38308400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:38298200-38313000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr17:38298200-38313600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:38298200-38318000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr17:38298200-38318200	Weak transcription	Small Intestine	intestine
19	chr17:38298200-38324200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr17:38298200-38324400	Strong transcription	Fetal Stomach	stomach
21	chr17:38298200-38333000	Strong transcription	Fetal Thymus	thymus
22	chr17:38298400-38324200	Weak transcription	Fetal Heart	heart
23	chr17:38298600-38309400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:38298600-38310600	Strong transcription	Lung	lung
25	chr17:38298600-38316400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:38298600-38319600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr17:38298600-38332200	Strong transcription	Fetal Intestine Small	intestine
28	chr17:38298800-38313200	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr17:38298800-38314000	Strong transcription	Fetal Muscle Leg	muscle
30	chr17:38299200-38319600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:38300000-38310200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr17:38300000-38312200	Strong transcription	Fetal Intestine Large	intestine
33	chr17:38301400-38313400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr17:38301600-38308400	Strong transcription	A549	lung
35	chr17:38301600-38324200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr17:38301800-38309800	Strong transcription	Fetal Brain Female	brain
37	chr17:38301800-38313200	Strong transcription	Placenta	Placenta
38	chr17:38301800-38313200	Strong transcription	Osteobl	bone
39	chr17:38301800-38324200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr17:38302200-38308400	Strong transcription	Primary T cells from cord blood	blood
41	chr17:38302200-38309600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr17:38302200-38312200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr17:38302200-38313200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr17:38302400-38312600	Strong transcription	Fetal Lung	lung
45	chr17:38302800-38310600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr17:38302800-38312400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr17:38302800-38313200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:38303000-38309600	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr17:38303000-38310800	Strong transcription	Esophagus	oesophagus
50	chr17:38303000-38324400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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