Variant report

Variant	rs9889905
Chromosome Location	chr17:38330605-38330606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr17:38330489-38330661	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr17:38330553-38331034	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr17:38330508-38330614	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:38330367-38331052	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38330070..38334400-chr17:38346938..38351108,4	K562	blood:
2	chr17:38296837..38298632-chr17:38328286..38330912,2	K562	blood:
3	chr17:38324296..38327279-chr17:38328642..38330964,3	K562	blood:
4	chr17:38177591..38179361-chr17:38330455..38332177,2	MCF-7	breast:

No data

Variant related genes	Relation type
RAPGEFL1	TF binding region
ENSG00000108352	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000108349	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10512482	0.85[EUR][1000 genomes]
rs1104761	0.92[EUR][1000 genomes]
rs11540720	0.85[EUR][1000 genomes]
rs12103533	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs15685	0.92[EUR][1000 genomes]
rs16965660	0.85[EUR][1000 genomes]
rs16965669	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16965734	0.85[EUR][1000 genomes]
rs16965736	0.85[EUR][1000 genomes]
rs16965748	0.85[EUR][1000 genomes]
rs16965774	0.85[EUR][1000 genomes]
rs16965778	0.85[EUR][1000 genomes]
rs17616543	0.92[EUR][1000 genomes]
rs17616672	0.92[EUR][1000 genomes]
rs17616879	0.92[EUR][1000 genomes]
rs17617263	0.92[EUR][1000 genomes]
rs17678817	0.92[EUR][1000 genomes]
rs17678959	0.92[EUR][1000 genomes]
rs17678990	0.92[EUR][1000 genomes]
rs17679086	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	0.85[EUR][1000 genomes]
rs28362321	0.92[EUR][1000 genomes]
rs28526298	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs33998939	0.92[EUR][1000 genomes]
rs34270904	0.85[EUR][1000 genomes]
rs34300454	0.85[EUR][1000 genomes]
rs35783632	0.92[EUR][1000 genomes]
rs35898909	0.92[EUR][1000 genomes]
rs41283417	0.85[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	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8071687	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8077482	0.85[EUR][1000 genomes]
rs9891944	0.92[EUR][1000 genomes]
rs9894364	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9894807	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9898500	0.85[EUR][1000 genomes]
rs9899425	0.85[EUR][1000 genomes]
rs9900154	0.85[EUR][1000 genomes]
rs9903293	0.85[EUR][1000 genomes]
rs9906274	0.92[EUR][1000 genomes]
rs9909777	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9909811	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9910373	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9915775	0.85[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38297800-38333000	Strong transcription	Fetal Muscle Trunk	muscle
2	chr17:38297800-38336600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:38298000-38330800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:38298200-38333000	Strong transcription	Fetal Thymus	thymus
5	chr17:38298600-38332200	Strong transcription	Fetal Intestine Small	intestine
6	chr17:38308200-38333200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr17:38314200-38333000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr17:38314800-38333200	Weak transcription	Right Atrium	heart
9	chr17:38315400-38331000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr17:38315400-38331400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr17:38315600-38333000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:38315600-38333000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:38315800-38331400	Strong transcription	Fetal Intestine Large	intestine
14	chr17:38316200-38333200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr17:38316400-38331400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr17:38317000-38333000	Strong transcription	Spleen	Spleen
17	chr17:38317200-38331000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr17:38317200-38333200	Strong transcription	Thymus	Thymus
19	chr17:38317400-38331200	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr17:38317400-38331400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr17:38317400-38333400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr17:38317400-38333800	Strong transcription	Dnd41	blood
23	chr17:38317600-38333000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr17:38317600-38333000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:38317600-38333200	Strong transcription	Left Ventricle	heart
26	chr17:38317800-38331400	Strong transcription	Lung	lung
27	chr17:38317800-38332800	Strong transcription	Brain Hippocampus Middle	brain
28	chr17:38318000-38331400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr17:38318000-38331400	Strong transcription	Brain Germinal Matrix	brain
30	chr17:38320600-38332800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:38321400-38331000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr17:38322400-38332000	Strong transcription	Fetal Brain Female	brain
33	chr17:38322400-38333200	Weak transcription	Psoas Muscle	Psoas
34	chr17:38323800-38332800	Strong transcription	Right Ventricle	heart
35	chr17:38324600-38332400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:38324600-38332800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr17:38324600-38333000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr17:38324800-38331200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr17:38324800-38331200	Strong transcription	Fetal Lung	lung
40	chr17:38324800-38331400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:38324800-38331400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr17:38324800-38332000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:38324800-38332200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr17:38324800-38332200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr17:38324800-38332800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:38324800-38333000	Strong transcription	Fetal Stomach	stomach
47	chr17:38324800-38333200	Strong transcription	Adipose Nuclei	Adipose
48	chr17:38325000-38331400	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr17:38325000-38332400	Strong transcription	Fetal Muscle Leg	muscle
50	chr17:38325000-38333000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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