Variant report

Variant	rs2289684
Chromosome Location	chr18:9619805-9619806
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	RAD21	chr18:9619346-9619950	IMR90	lung:	n/a	n/a
2	POLR2A	chr18:9619538-9619805	HUVEC	blood vessel:	n/a	n/a
3	MAFK	chr18:9619219-9619980	IMR90	lung:	n/a	n/a
4	FOS	chr18:9619282-9619989	HUVEC	blood vessel:	n/a	n/a
5	GATA2	chr18:9619202-9619985	HUVEC	blood vessel:	n/a	n/a
6	RUNX3	chr18:9619555-9619860	GM12878	blood:	n/a	n/a
7	POLR2A	chr18:9619641-9620023	IMR90	lung:	n/a	n/a
8	POLR2A	chr18:9619442-9619932	HUVEC	blood vessel:	n/a	n/a
9	FOS	chr18:9619637-9619849	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr18:9619429-9620429	IMR90	lung:	n/a	chr18:9620226-9620237
11	RUNX3	chr18:9619560-9619944	GM12878	blood:	n/a	n/a
12	POLR2A	chr18:9619689-9619862	HUVEC	blood vessel:	n/a	n/a
13	RCOR1	chr18:9619631-9620436	K562	blood:	n/a	n/a
14	FOS	chr18:9619697-9619859	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr18:9619319-9619945	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr18:9619552-9619965	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9612628..9617891-chr18:9619605..9623342,5	MCF-7	breast:
2	chr18:9614482..9616420-chr18:9617986..9621274,5	K562	blood:

Variant related genes	Relation type
PPP4R1	TF binding region
RNU6-903P	TF binding region
ENSG00000263627	Chromatin interaction
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11081489	0.81[ASN][1000 genomes]
rs1662885	0.89[ASN][1000 genomes]
rs1787165	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2028661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs328995	1.00[CHB][hapmap]
rs329002	1.00[ASN][1000 genomes]
rs329004	1.00[ASN][1000 genomes]
rs329008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs329023	0.90[ASN][1000 genomes]
rs329024	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs329033	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35444634	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs428598	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586544	0.81[ASN][1000 genomes]
rs589559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs599861	1.00[ASN][1000 genomes]
rs610564	0.82[ASN][1000 genomes]
rs62088920	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs633907	0.85[CHB][hapmap]
rs638578	0.89[ASN][1000 genomes]
rs667695	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671339	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677461	0.85[ASN][1000 genomes]
rs680478	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683319	0.81[ASN][1000 genomes]
rs694861	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs7233160	1.00[ASN][1000 genomes]
rs7234128	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7359735	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8088389	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8090919	0.89[ASN][1000 genomes]
rs9807577	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9807604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807610	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9807614	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9950583	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2289684	RP11-692N5.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2289684	RP11-692N5.1	cis	Esophagus Mucosa	GTEx
rs2289684	RP11-692N5.1	cis	Esophagus Muscularis	GTEx
rs2289684	RP11-692N5.1	cis	Nerve Tibial	GTEx
rs2289684	RP11-692N5.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9615800-9625200	Weak transcription	Placenta	Placenta
2	chr18:9615800-9625400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr18:9615800-9627400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr18:9617400-9625400	Weak transcription	HMEC	breast
5	chr18:9617600-9630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:9618800-9620200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr18:9619000-9620000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr18:9619200-9620000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr18:9619200-9620000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr18:9619200-9620000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr18:9619200-9620000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr18:9619200-9620000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr18:9619200-9620000	Enhancers	Brain Anterior Caudate	brain
14	chr18:9619200-9620000	Enhancers	Duodenum Mucosa	Duodenum
15	chr18:9619200-9620000	Enhancers	GM12878-XiMat	blood
16	chr18:9619200-9620000	Enhancers	Hela-S3	cervix
17	chr18:9619200-9620000	Enhancers	NHDF-Ad	bronchial
18	chr18:9619200-9620200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr18:9619200-9620200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr18:9619200-9620200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr18:9619200-9620200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr18:9619200-9620200	Flanking Active TSS	HUVEC	blood vessel
23	chr18:9619200-9620200	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr18:9619200-9620200	Enhancers	NHEK	skin
25	chr18:9619200-9620200	Enhancers	NHLF	lung
26	chr18:9619400-9620000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr18:9619400-9620000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr18:9619400-9620000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr18:9619400-9620000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr18:9619400-9620000	Enhancers	Dnd41	blood
31	chr18:9619400-9620200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr18:9619400-9620200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr18:9619400-9620200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr18:9619600-9620000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr18:9619600-9620000	Enhancers	Fetal Lung	lung
36	chr18:9619600-9620200	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr18:9619600-9620200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr18:9619600-9620200	Enhancers	HSMM	muscle
39	chr18:9619600-9620200	Enhancers	Osteobl	bone
40	chr18:9619600-9620400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr18:9619800-9620000	Enhancers	Brain Hippocampus Middle	brain
42	chr18:9619800-9620000	Enhancers	K562	blood
43	chr18:9619800-9620000	Flanking Active TSS	NH-A	brain
44	chr18:9619800-9620200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr18:9619800-9620200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr18:9619800-9620200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr18:9619800-9620200	Enhancers	A549	lung
48	chr18:9619800-9627400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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