Variant report

Variant	rs62088915
Chromosome Location	chr18:9616980-9616981
allele	A/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	ARID3A	chr18:9616735-9617052	K562	blood:	n/a	n/a
2	EP300	chr18:9616929-9617099	GM12878	blood:	n/a	chr18:9616996-9617010
3	GATA1	chr18:9615396-9617194	PBDE	blood:	n/a	n/a
4	POLR2A	chr18:9616500-9617170	MCF10A-Er-Src	breast:	n/a	n/a
5	IRF1	chr18:9616786-9617198	K562	blood:	n/a	chr18:9616995-9617005 chr18:9616995-9617009
6	ZNF384	chr18:9616798-9617006	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9616424..9618415-chr18:9912586..9915951,3	MCF-7	breast:
2	chr18:9614624..9617257-chr18:9707449..9709089,2	K562	blood:
3	chr18:9615287..9617165-chr18:9631128..9633561,2	K562	blood:
4	chr18:9615576..9617257-chr18:9706860..9708949,2	K562	blood:
5	chr18:9596087..9600746-chr18:9613522..9617540,6	MCF-7	breast:
6	chr18:9612544..9617098-chr18:9708301..9712595,6	MCF-7	breast:
7	chr18:9615456..9617526-chr18:9895448..9898198,2	K562	blood:

Variant related genes	Relation type
PPP4R1	TF binding region
ENSG00000272799	Chromatin interaction
ENSG00000154845	Chromatin interaction
ENSG00000168461	Chromatin interaction
ENSG00000101558	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs61746389	1.00[EUR][1000 genomes]
rs61749090	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61749091	1.00[EUR][1000 genomes]
rs62080294	0.93[EUR][1000 genomes]
rs62080298	0.96[EUR][1000 genomes]
rs62080299	0.96[EUR][1000 genomes]
rs62080302	0.96[EUR][1000 genomes]
rs62080303	0.96[EUR][1000 genomes]
rs62080304	0.89[EUR][1000 genomes]
rs62080305	0.90[EUR][1000 genomes]
rs62087424	0.82[EUR][1000 genomes]
rs62087455	0.82[EUR][1000 genomes]
rs62087457	0.82[EUR][1000 genomes]
rs62087458	0.82[EUR][1000 genomes]
rs62088862	0.82[EUR][1000 genomes]
rs62088863	0.82[EUR][1000 genomes]
rs62088865	0.82[EUR][1000 genomes]
rs62088866	0.84[EUR][1000 genomes]
rs62088867	0.84[EUR][1000 genomes]
rs62088869	0.84[EUR][1000 genomes]
rs62088874	0.81[EUR][1000 genomes]
rs62088882	0.85[EUR][1000 genomes]
rs62088909	0.85[EUR][1000 genomes]
rs62088910	0.90[EUR][1000 genomes]
rs62088911	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62088912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62088913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62088914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62088917	0.97[EUR][1000 genomes]
rs62088918	1.00[EUR][1000 genomes]
rs7236182	0.92[AMR][1000 genomes];0.96[EUR][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	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv1820504	chr18:9614250-9621841	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv1801741	chr18:9614451-9621841	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv521175	chr18:9615851-9623052	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62088915	RP11-692N5.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9615400-9618200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:9615600-9617000	Enhancers	Brain Substantia Nigra	brain
3	chr18:9615600-9617000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr18:9615600-9617200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:9615600-9617400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr18:9615600-9617600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr18:9615600-9617600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr18:9615600-9619200	Weak transcription	GM12878-XiMat	blood
9	chr18:9615800-9617000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr18:9615800-9617000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr18:9615800-9617000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr18:9615800-9617000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr18:9615800-9617000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr18:9615800-9617000	Enhancers	A549	lung
15	chr18:9615800-9617000	Enhancers	HepG2	liver
16	chr18:9615800-9617400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:9615800-9617400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr18:9615800-9617400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr18:9615800-9617400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr18:9615800-9617400	Enhancers	Dnd41	blood
21	chr18:9615800-9617400	Enhancers	Hela-S3	cervix
22	chr18:9615800-9617400	Enhancers	HSMM	muscle
23	chr18:9615800-9617400	Enhancers	NHDF-Ad	bronchial
24	chr18:9615800-9617400	Enhancers	NHLF	lung
25	chr18:9615800-9617400	Enhancers	Osteobl	bone
26	chr18:9615800-9617600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr18:9615800-9617600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr18:9615800-9617600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr18:9615800-9617600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:9615800-9617600	Enhancers	NHEK	skin
31	chr18:9615800-9619200	Weak transcription	Brain Angular Gyrus	brain
32	chr18:9615800-9619200	Weak transcription	Brain Anterior Caudate	brain
33	chr18:9615800-9619200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr18:9615800-9619200	Weak transcription	Esophagus	oesophagus
35	chr18:9615800-9619200	Enhancers	HUVEC	blood vessel
36	chr18:9615800-9619400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr18:9615800-9619400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr18:9615800-9619600	Weak transcription	Fetal Lung	lung
39	chr18:9615800-9619800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr18:9615800-9625200	Weak transcription	Placenta	Placenta
41	chr18:9615800-9625400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr18:9615800-9627400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr18:9616000-9617400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr18:9616000-9617400	Enhancers	HMEC	breast
45	chr18:9616000-9617600	Enhancers	Brain Cingulate Gyrus	brain
46	chr18:9616000-9618800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr18:9616000-9619200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr18:9616000-9619200	Weak transcription	Stomach Mucosa	stomach
49	chr18:9616000-9619200	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr18:9616000-9619800	Weak transcription	Brain Hippocampus Middle	brain

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