Variant report

Variant	rs10733584
Chromosome Location	chr9:100002036-100002037
allele	A/C/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	chr9:100001822-100002175	K562	blood:	n/a	n/a
2	GATA3	chr9:100001883-100002207	SH-SY5Y	brain:	n/a	n/a
3	HCFC1	chr9:100000074-100002060	Hela-S3	cervix:	n/a	n/a
4	GATA2	chr9:100001836-100002172	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000203279	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10115798	0.90[EUR][1000 genomes]
rs10116404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217229	0.87[EUR][1000 genomes]
rs10217329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10435866	0.80[EUR][1000 genomes]
rs10733603	0.80[EUR][1000 genomes]
rs10739337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739365	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759605	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759610	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759619	0.81[EUR][1000 genomes]
rs10817300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817361	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10817403	0.86[ASN][1000 genomes]
rs10817448	0.82[EUR][1000 genomes]
rs10981362	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981528	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981537	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981551	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981557	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981560	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981625	0.83[EUR][1000 genomes]
rs12683119	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12683933	0.80[AMR][1000 genomes]
rs1462086	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1462087	0.82[EUR][1000 genomes]
rs1462092	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1531439	0.80[AMR][1000 genomes]
rs1857084	0.85[ASN][1000 genomes]
rs1870859	0.83[EUR][1000 genomes]
rs1935372	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061634	0.82[EUR][1000 genomes]
rs2061635	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2255135	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255139	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255244	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2401382	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447287	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447288	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447289	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447290	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2487874	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2487875	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2502646	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2615144	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795363	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795366	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795369	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795370	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818236	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818237	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818240	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818241	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818242	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818244	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2859564	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2888960	0.88[EUR][1000 genomes]
rs3953688	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3994559	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3994561	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3994562	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4345679	0.83[EUR][1000 genomes]
rs4433262	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4437755	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4507886	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4524907	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4615708	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4645658	0.82[EUR][1000 genomes]
rs4742683	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4742684	0.82[EUR][1000 genomes]
rs4743067	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4743074	0.83[EUR][1000 genomes]
rs4743075	0.82[EUR][1000 genomes]
rs6477982	0.85[ASN][1000 genomes]
rs6477988	0.85[ASN][1000 genomes]
rs6477993	0.85[ASN][1000 genomes]
rs6478008	0.84[AMR][1000 genomes]
rs6478043	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478044	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478048	0.87[EUR][1000 genomes]
rs6478051	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478054	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478055	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478059	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7020002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020144	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021895	0.84[AMR][1000 genomes]
rs7023087	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026287	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026893	0.82[EUR][1000 genomes]
rs7029749	0.80[EUR][1000 genomes]
rs7033212	0.91[EUR][1000 genomes]
rs7033480	0.85[EUR][1000 genomes]
rs7033642	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7036964	0.83[EUR][1000 genomes]
rs7038353	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047367	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71491754	0.85[EUR][1000 genomes]
rs725228	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs725229	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs752243	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7847332	0.80[EUR][1000 genomes]
rs7850473	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7855385	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855956	0.81[EUR][1000 genomes]
rs7860264	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7867330	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7868052	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868295	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868312	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7875158	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7875296	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9299202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9408859	0.87[EUR][1000 genomes]
rs9409139	0.88[EUR][1000 genomes];0.86[ASN][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	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10733584	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs10733584	CCDC180	cis	Artery Tibial	GTEx
rs10733584	RP11-23J9.4	cis	Artery Tibial	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99998600-100002200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr9:100001200-100011000	Weak transcription	Lung	lung
3	chr9:100001200-100017000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:100001200-100039400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:100001400-100002200	Enhancers	Liver	Liver
6	chr9:100001400-100003600	Weak transcription	Aorta	Aorta
7	chr9:100001400-100003800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:100001400-100005800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:100001400-100010800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:100001400-100014000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr9:100001400-100017600	Weak transcription	Left Ventricle	heart
12	chr9:100001400-100017800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:100001600-100002200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:100001600-100002200	Flanking Active TSS	Hela-S3	cervix
15	chr9:100001600-100002400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr9:100001600-100002400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr9:100001600-100002400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:100001600-100003800	Weak transcription	NH-A	brain
19	chr9:100001600-100005800	Weak transcription	NHEK	skin
20	chr9:100001600-100012800	Weak transcription	Fetal Kidney	kidney
21	chr9:100001600-100014000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:100001600-100022200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:100001600-100037400	Weak transcription	Primary T cells from cord blood	blood
24	chr9:100001800-100002200	Enhancers	Brain Hippocampus Middle	brain
25	chr9:100001800-100002200	Enhancers	Brain Substantia Nigra	brain
26	chr9:100001800-100002200	Flanking Active TSS	K562	blood
27	chr9:100001800-100004600	Weak transcription	Fetal Lung	lung
28	chr9:100001800-100005600	Weak transcription	Osteobl	bone
29	chr9:100001800-100005800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:100001800-100012800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr9:100002000-100002200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr9:100002000-100002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:100002000-100002200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr9:100002000-100002200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:100002000-100002200	Enhancers	Brain Cingulate Gyrus	brain
36	chr9:100002000-100002400	Enhancers	Brain Germinal Matrix	brain
37	chr9:100002000-100003000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr9:100002000-100003200	Enhancers	Dnd41	blood
39	chr9:100002000-100004200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr9:100002000-100005000	Weak transcription	Brain Anterior Caudate	brain
41	chr9:100002000-100005600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:100002000-100005800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:100002000-100010400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr9:100002000-100011000	Weak transcription	Fetal Stomach	stomach
45	chr9:100002000-100011600	Weak transcription	Pancreas	Pancrea
46	chr9:100002000-100013200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr9:100002000-100013400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr9:100002000-100015200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:100002000-100016600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr9:100002000-100016600	Weak transcription	Thymus	Thymus

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