Variant report

Variant	rs67450563
Chromosome Location	chr18:11998302-11998303
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	REST	chr18:11998219-11998677	ECC-1	luminal epithelium:	n/a	chr18:11998367-11998380 chr18:11998468-11998477 chr18:11998364-11998377 chr18:11998463-11998483
2	POLR2A	chr18:11993400-11998536	Hela-S3	cervix:	n/a	n/a
3	REST	chr18:11998158-11998586	ECC-1	luminal epithelium:	n/a	chr18:11998367-11998380 chr18:11998468-11998477 chr18:11998364-11998377 chr18:11998463-11998483

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:11978568..11983192-chr18:11993805..11998306,5	MCF-7	breast:

Variant related genes	Relation type
IMPA2	TF binding region
ENSG00000266955	TF binding region
ENSG00000141401	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11545506	0.85[AFR][1000 genomes]
rs11660567	0.84[ASN][1000 genomes]
rs16976887	0.85[ASN][1000 genomes]
rs28475846	0.85[ASN][1000 genomes]
rs28499558	0.85[ASN][1000 genomes]
rs28509217	0.85[ASN][1000 genomes]
rs28548932	0.85[ASN][1000 genomes]
rs4239304	0.85[ASN][1000 genomes]
rs56364728	0.85[ASN][1000 genomes]
rs57967783	0.85[ASN][1000 genomes]
rs58556096	0.83[ASN][1000 genomes]
rs59796048	0.85[ASN][1000 genomes]
rs59889312	0.85[ASN][1000 genomes]
rs6505700	0.85[ASN][1000 genomes]
rs6505701	0.85[ASN][1000 genomes]
rs67932171	0.85[ASN][1000 genomes]
rs7230346	0.85[ASN][1000 genomes]
rs7240032	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7244678	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72871698	0.85[ASN][1000 genomes]
rs72871700	0.85[ASN][1000 genomes]
rs72871702	0.85[ASN][1000 genomes]
rs72873509	0.85[ASN][1000 genomes]
rs72873510	0.85[ASN][1000 genomes]
rs72873549	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7407928	0.85[ASN][1000 genomes]
rs7506045	0.85[ASN][1000 genomes]
rs9973177	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982400-12005000	Weak transcription	Aorta	Aorta
2	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
3	chr18:11991000-11999200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr18:11993200-11998400	Enhancers	Fetal Muscle Trunk	muscle
5	chr18:11993400-11999400	Enhancers	Fetal Muscle Leg	muscle
6	chr18:11993400-12016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr18:11995000-11999200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:11995400-11998400	Enhancers	Brain Hippocampus Middle	brain
9	chr18:11995400-11999200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:11995400-12001800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:11995600-11998600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr18:11995600-11998800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr18:11995600-11999000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr18:11995600-11999000	Weak transcription	Fetal Brain Female	brain
15	chr18:11995600-11999200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr18:11995600-11999400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr18:11995600-12014400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr18:11995800-11999000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr18:11995800-11999400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr18:11996000-11998600	Weak transcription	HSMM	muscle
21	chr18:11996000-11999200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr18:11996000-11999200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:11996000-11999200	Weak transcription	Fetal Intestine Large	intestine
24	chr18:11996000-11999200	Enhancers	HepG2	liver
25	chr18:11996000-12001400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr18:11996000-12001400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr18:11996000-12004000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr18:11996000-12004800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr18:11996000-12004800	Weak transcription	HMEC	breast
30	chr18:11996000-12005600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr18:11996200-11998400	Weak transcription	Fetal Kidney	kidney
32	chr18:11996200-11998400	Enhancers	Lung	lung
33	chr18:11996200-11999000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr18:11996200-11999000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr18:11996200-11999000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr18:11996200-11999000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr18:11996200-11999000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr18:11996200-11999200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr18:11996200-11999200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr18:11996200-11999400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr18:11996200-11999600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr18:11996200-12004800	Weak transcription	NHEK	skin
43	chr18:11996200-12005200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr18:11996200-12005600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr18:11996200-12012200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr18:11996200-12014800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr18:11996200-12015400	Weak transcription	Brain Anterior Caudate	brain
48	chr18:11996400-11998400	Enhancers	Psoas Muscle	Psoas
49	chr18:11996400-11998400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr18:11996400-11999000	Weak transcription	A549	lung

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