Variant report

Variant	rs7048509
Chromosome Location	chr9:14992582-14992583
allele	A/T
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	IRF1	chr9:14991634-14993552	K562	blood:	n/a	chr9:14993194-14993208 chr9:14993205-14993219 chr9:14992210-14992231
2	MXI1	chr9:14991869-14994541	SK-N-SH	brain:	n/a	n/a
3	RFX5	chr9:14991332-14994287	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr9:14992024-14992932	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr9:14992199-14993642	K562	blood:	n/a	n/a
6	IRF1	chr9:14991870-14993516	K562	blood:	n/a	chr9:14993194-14993208 chr9:14993205-14993219 chr9:14992210-14992231
7	POLR2A	chr9:14992129-14994373	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr9:14992494-14992667	K562	blood:	n/a	n/a
9	POLR2A	chr9:14992157-14992786	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000215237	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10114147	0.83[EUR][1000 genomes]
rs10511603	0.88[ASN][1000 genomes]
rs10511604	0.82[ASN][1000 genomes]
rs10756632	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10756635	0.88[ASN][1000 genomes]
rs10756636	0.88[ASN][1000 genomes]
rs10756637	0.88[ASN][1000 genomes]
rs10810297	0.84[EUR][1000 genomes]
rs10810298	0.84[EUR][1000 genomes]
rs10810307	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810308	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810309	1.00[ASN][1000 genomes]
rs10810310	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10810311	0.94[ASN][1000 genomes]
rs10810312	0.94[ASN][1000 genomes]
rs10810314	0.90[ASN][1000 genomes]
rs10810315	0.89[ASN][1000 genomes]
rs10810316	0.88[ASN][1000 genomes]
rs10810317	0.88[ASN][1000 genomes]
rs10810318	0.82[ASN][1000 genomes]
rs10810319	0.81[ASN][1000 genomes]
rs10810320	0.88[ASN][1000 genomes]
rs10810321	0.88[ASN][1000 genomes]
rs10810323	0.88[ASN][1000 genomes]
rs10810326	0.88[ASN][1000 genomes]
rs10810327	0.88[ASN][1000 genomes]
rs10961817	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10961819	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10961820	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10961825	0.91[ASN][1000 genomes]
rs10961826	0.91[ASN][1000 genomes]
rs10961827	0.88[ASN][1000 genomes]
rs10961828	0.88[ASN][1000 genomes]
rs10961831	0.88[ASN][1000 genomes]
rs10961832	0.88[ASN][1000 genomes]
rs11788817	0.88[ASN][1000 genomes]
rs11793253	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12335682	0.94[ASN][1000 genomes]
rs12340301	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12343244	0.83[ASN][1000 genomes]
rs12344181	0.83[ASN][1000 genomes]
rs12352024	0.85[ASN][1000 genomes]
rs12379705	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1357474	0.84[EUR][1000 genomes]
rs1412720	0.82[EUR][1000 genomes]
rs1464608	0.82[EUR][1000 genomes]
rs1589666	0.84[EUR][1000 genomes]
rs17223865	0.83[ASN][1000 genomes]
rs1829850	0.84[EUR][1000 genomes]
rs1851588	0.90[ASN][1000 genomes]
rs1851590	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1880012	0.87[EUR][1000 genomes]
rs1880013	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1916311	0.88[ASN][1000 genomes]
rs1916312	0.88[ASN][1000 genomes]
rs1916313	0.83[ASN][1000 genomes]
rs2011091	0.88[ASN][1000 genomes]
rs2049291	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2140322	0.85[EUR][1000 genomes]
rs2381973	0.84[EUR][1000 genomes]
rs2382508	0.83[ASN][1000 genomes]
rs4008009	0.83[EUR][1000 genomes]
rs4535838	0.82[EUR][1000 genomes]
rs4548277	0.87[EUR][1000 genomes]
rs4553007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57255198	0.88[ASN][1000 genomes]
rs62536769	0.91[ASN][1000 genomes]
rs6474876	0.85[EUR][1000 genomes]
rs6474878	0.80[EUR][1000 genomes]
rs7018678	0.87[EUR][1000 genomes]
rs7020107	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7026072	0.83[EUR][1000 genomes]
rs7028104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028135	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7028702	0.91[EUR][1000 genomes]
rs7030516	0.86[EUR][1000 genomes]
rs7037967	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7040712	0.87[EUR][1000 genomes]
rs7042782	0.84[EUR][1000 genomes]
rs7046824	0.81[EUR][1000 genomes]
rs7350286	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7350287	0.84[EUR][1000 genomes]
rs7848747	0.80[EUR][1000 genomes]
rs7855093	0.85[EUR][1000 genomes]
rs7858719	0.88[ASN][1000 genomes]
rs7858723	0.88[ASN][1000 genomes]
rs9298710	0.83[EUR][1000 genomes]
rs940118	0.88[ASN][1000 genomes]
rs9886740	0.88[ASN][1000 genomes]
rs9886864	0.88[ASN][1000 genomes]
rs9886867	0.88[ASN][1000 genomes]
rs9886868	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv613647	chr9:14852141-15016475	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv892620	chr9:14922877-15086021	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv892621	chr9:14928013-15043692	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2761503	chr9:14960217-15049343	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv892622	chr9:14960217-15055607	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7048509	RP11-54D18.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14982200-14992600	Weak transcription	Fetal Lung	lung
2	chr9:14990000-14992800	Weak transcription	NH-A	brain
3	chr9:14991400-14992800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr9:14991600-14992600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:14991600-14993800	Active TSS	K562	blood
6	chr9:14991600-14994400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:14991800-14994400	Active TSS	NHDF-Ad	bronchial
8	chr9:14992000-14992600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:14992000-14992800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr9:14992000-14993000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:14992000-14994000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:14992000-14994200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr9:14992000-14994200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr9:14992000-14994400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr9:14992200-14992600	Active TSS	Colon Smooth Muscle	Colon
16	chr9:14992200-14992600	Active TSS	Hela-S3	cervix
17	chr9:14992200-14992800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:14992200-14992800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:14992200-14992800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:14992200-14993000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr9:14992200-14993000	Enhancers	Fetal Thymus	thymus
22	chr9:14992200-14993200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr9:14992200-14993200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr9:14992200-14993200	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr9:14992200-14993400	Active TSS	Placenta	Placenta
26	chr9:14992200-14993600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr9:14992200-14994000	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr9:14992200-14994000	Active TSS	Aorta	Aorta
29	chr9:14992200-14994000	Active TSS	Right Atrium	heart
30	chr9:14992200-14994400	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr9:14992200-14994800	Active TSS	Psoas Muscle	Psoas
32	chr9:14992200-14995000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:14992400-14992600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr9:14992400-14992600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr9:14992400-14992600	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr9:14992400-14992600	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr9:14992400-14992600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:14992400-14992600	Active TSS	Duodenum Mucosa	Duodenum
39	chr9:14992400-14992600	Enhancers	Fetal Heart	heart
40	chr9:14992400-14992800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
41	chr9:14992400-14992800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr9:14992400-14992800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:14992400-14992800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr9:14992400-14992800	Enhancers	Primary T cells from cord blood	blood
45	chr9:14992400-14992800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:14992400-14992800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr9:14992400-14992800	Flanking Active TSS	Thymus	Thymus
48	chr9:14992400-14993000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr9:14992400-14993000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr9:14992400-14993000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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