Variant report

Variant	rs4797687
Chromosome Location	chr18:12443067-12443068
allele	C/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	FOS	chr18:12443025-12443288	MCF10A-Er-Src	breast:	n/a	chr18:12443147-12443157 chr18:12443147-12443157 chr18:12443147-12443157
2	POLR2A	chr18:12443047-12443242	A549	lung:	n/a	n/a
3	FOS	chr18:12443010-12443296	MCF10A-Er-Src	breast:	n/a	chr18:12443147-12443157 chr18:12443147-12443157 chr18:12443147-12443157
4	POLR2A	chr18:12443018-12444650	K562	blood:	n/a	n/a
5	CEBPB	chr18:12442969-12443302	IMR90	lung:	n/a	n/a
6	FOS	chr18:12442992-12443256	MCF10A-Er-Src	breast:	n/a	chr18:12443147-12443157 chr18:12443147-12443157 chr18:12443147-12443157
7	FOS	chr18:12442952-12443345	HUVEC	blood vessel:	n/a	chr18:12443147-12443157 chr18:12443147-12443157 chr18:12443147-12443157

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12436823..12439176-chr18:12440236..12443079,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLMO1-1	chr18:12442971-12443271	ENSG00000267199.1

Variant related genes	Relation type
ENSG00000267199	TF binding region
ENSG00000267199	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11664219	0.85[CEU][hapmap]
rs11664232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11665415	0.85[CEU][hapmap]
rs11665542	0.85[CEU][hapmap]
rs16973057	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16977205	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[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16977214	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16977227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1893236	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2040197	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3887990	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4566245	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[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4797689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4797693	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56723469	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58500351	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73403752	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73403754	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73403761	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73403763	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73949246	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9959201	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12420600-12443600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr18:12421200-12443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr18:12421200-12447600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr18:12421200-12452800	Weak transcription	Colonic Mucosa	Colon
6	chr18:12421400-12444200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr18:12428400-12443400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr18:12428600-12443800	Weak transcription	HSMMtube	muscle
9	chr18:12430800-12443400	Weak transcription	A549	lung
10	chr18:12431000-12443400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:12431000-12443600	Weak transcription	Fetal Heart	heart
12	chr18:12431000-12447600	Weak transcription	NH-A	brain
13	chr18:12431000-12449200	Weak transcription	Pancreas	Pancrea
14	chr18:12431200-12443400	Weak transcription	Fetal Kidney	kidney
15	chr18:12431200-12447800	Weak transcription	NHEK	skin
16	chr18:12431400-12443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:12432000-12443800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr18:12432600-12447000	Weak transcription	HMEC	breast
19	chr18:12433000-12443200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr18:12433000-12443600	Weak transcription	Fetal Brain Male	brain
21	chr18:12433000-12448800	Weak transcription	HUVEC	blood vessel
22	chr18:12433200-12443400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:12433200-12443400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr18:12433200-12443600	Weak transcription	Brain Angular Gyrus	brain
25	chr18:12433200-12444000	Weak transcription	Left Ventricle	heart
26	chr18:12433200-12444000	Weak transcription	Right Ventricle	heart
27	chr18:12433200-12449200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr18:12433200-12449200	Weak transcription	Gastric	stomach
29	chr18:12433200-12449200	Weak transcription	Spleen	Spleen
30	chr18:12433200-12450200	Weak transcription	Thymus	Thymus
31	chr18:12433200-12464600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr18:12433400-12443600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr18:12433400-12458600	Weak transcription	HepG2	liver
34	chr18:12434200-12443600	Weak transcription	Fetal Intestine Large	intestine
35	chr18:12434200-12477000	Weak transcription	Esophagus	oesophagus
36	chr18:12434600-12443400	Weak transcription	Ovary	ovary
37	chr18:12434800-12443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr18:12435000-12443400	Weak transcription	Adipose Nuclei	Adipose
39	chr18:12435000-12443400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr18:12435000-12443800	Weak transcription	Brain Hippocampus Middle	brain
41	chr18:12435000-12444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr18:12435000-12444000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr18:12435200-12443600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr18:12435200-12443600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr18:12435200-12444200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr18:12435200-12449000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr18:12436400-12443600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr18:12438200-12449200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr18:12438600-12443200	Weak transcription	HSMM	muscle
50	chr18:12438600-12443600	Weak transcription	Stomach Smooth Muscle	stomach

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