Variant report

Variant	rs11540888
Chromosome Location	chr17:18159891-18159892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr17:18159605-18160097	A549	lung:	n/a	n/a
2	REST	chr17:18159654-18160035	U87	brain:	n/a	n/a
3	REST	chr17:18159773-18159921	K562	blood:	n/a	n/a
4	REST	chr17:18159640-18160085	ECC-1	luminal epithelium:	n/a	n/a
5	REST	chr17:18159703-18159903	Hela-S3	cervix:	n/a	n/a
6	REST	chr17:18159656-18160035	U87	brain:	n/a	n/a
7	REST	chr17:18159698-18159969	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr17:18159719-18159943	HepG2	liver:	n/a	n/a
9	REST	chr17:18159644-18160159	ECC-1	luminal epithelium:	n/a	n/a
10	REST	chr17:18159641-18160057	HepG2	liver:	n/a	n/a
11	REST	chr17:18159725-18159994	PFSK-1	brain:	n/a	n/a
12	REST	chr17:18159695-18159965	K562	blood:	n/a	n/a
13	REST	chr17:18159639-18159935	PANC-1	pancreas:	n/a	n/a
14	REST	chr17:18159693-18160033	A549	lung:	n/a	n/a
15	REST	chr17:18159722-18159941	HepG2	liver:	n/a	n/a
16	REST	chr17:18159673-18159999	H1-hESC	embryonic stem cell:	n/a	n/a
17	REST	chr17:18159713-18159948	SK-N-SH	brain:	n/a	n/a
18	REST	chr17:18159718-18159929	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18127100..18135567-chr17:18158023..18168767,25	MCF-7	breast:
2	chr17:18156705..18166530-chr17:18215131..18220177,19	MCF-7	breast:
3	chr17:18126073..18132705-chr17:18158327..18165323,14	MCF-7	breast:
4	chr17:18158849..18161472-chr17:18226331..18228845,2	MCF-7	breast:
5	chr17:18158589..18161919-chr17:18164225..18167330,4	K562	blood:
6	chr17:18159414..18161817-chr17:18169101..18171467,2	K562	blood:
7	chr17:18159194..18166260-chr17:18215929..18222740,16	MCF-7	breast:

No data

Variant related genes	Relation type
MIEF2	TF binding region
FLII	TF binding region
ENSG00000267350	Chromatin interaction
ENSG00000131899	Chromatin interaction
ENSG00000176994	Chromatin interaction
ENSG00000177427	Chromatin interaction
ENSG00000237382	Chromatin interaction
ENSG00000260647	Chromatin interaction
ENSG00000228000	Chromatin interaction
ENSG00000177302	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11870681	1.00[ASN][1000 genomes]
rs16961058	1.00[ASN][1000 genomes]
rs16961112	1.00[ASN][1000 genomes]
rs2125154	1.00[ASN][1000 genomes]
rs28671051	1.00[ASN][1000 genomes]
rs4924848	1.00[ASN][1000 genomes]
rs4925170	1.00[ASN][1000 genomes]
rs4925173	1.00[ASN][1000 genomes]
rs4925175	1.00[ASN][1000 genomes]
rs4925180	1.00[ASN][1000 genomes]
rs55973639	1.00[ASN][1000 genomes]
rs61753153	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502648	1.00[ASN][1000 genomes]
rs7215491	1.00[ASN][1000 genomes]
rs7222589	1.00[ASN][1000 genomes]
rs73980813	1.00[ASN][1000 genomes]
rs73980819	1.00[ASN][1000 genomes]
rs73980849	1.00[ASN][1000 genomes]
rs73980856	1.00[ASN][1000 genomes]
rs73980857	1.00[ASN][1000 genomes]
rs8074858	1.00[ASN][1000 genomes]
rs8080285	1.00[ASN][1000 genomes]
rs8082574	1.00[ASN][1000 genomes]
rs9893254	1.00[ASN][1000 genomes]
rs9894005	1.00[ASN][1000 genomes]
rs9894616	1.00[ASN][1000 genomes]
rs9902011	1.00[ASN][1000 genomes]
rs9902498	1.00[ASN][1000 genomes]
rs9903762	1.00[ASN][1000 genomes]
rs9913916	1.00[ASN][1000 genomes]
rs9915858	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv543246	chr17:18121007-18165604	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
10	nsv9503	chr17:18121474-18169166	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
11	nsv907776	chr17:18122485-18170948	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
12	nsv1066718	chr17:18125122-18180807	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv907777	chr17:18131087-18163262	Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18135200-18160000	Strong transcription	Fetal Brain Female	brain
2	chr17:18135400-18160200	Strong transcription	Thymus	Thymus
3	chr17:18135600-18160000	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr17:18135800-18160400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:18136000-18160000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:18136200-18160000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:18136200-18160000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:18139800-18160000	Strong transcription	Osteobl	bone
9	chr17:18139800-18160200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:18140000-18160000	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr17:18143400-18160200	Strong transcription	NHLF	lung
12	chr17:18143600-18160000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:18143800-18160000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:18143800-18160200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr17:18144000-18160000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:18144000-18160200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr17:18144200-18160000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr17:18146600-18160000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr17:18148200-18160200	Strong transcription	Aorta	Aorta
20	chr17:18150800-18160000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:18150800-18160000	Strong transcription	Fetal Intestine Large	intestine
22	chr17:18150800-18160000	Strong transcription	HSMM	muscle
23	chr17:18151000-18160000	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr17:18151200-18160000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:18151200-18160000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr17:18151200-18160000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr17:18151200-18160000	Weak transcription	Fetal Brain Male	brain
28	chr17:18151200-18160200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr17:18151200-18160200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr17:18151200-18160400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr17:18151400-18160000	Strong transcription	Placenta	Placenta
32	chr17:18151400-18160600	Weak transcription	K562	blood
33	chr17:18152000-18160000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr17:18152200-18160000	Strong transcription	Brain Anterior Caudate	brain
35	chr17:18152200-18160200	Strong transcription	Fetal Intestine Small	intestine
36	chr17:18152200-18160200	Strong transcription	A549	lung
37	chr17:18152400-18160000	Strong transcription	Colonic Mucosa	Colon
38	chr17:18152400-18160000	Strong transcription	Ovary	ovary
39	chr17:18152400-18160000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr17:18152600-18160000	Strong transcription	Brain Hippocampus Middle	brain
41	chr17:18152600-18160000	Strong transcription	Fetal Stomach	stomach
42	chr17:18152800-18160000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:18152800-18160000	Strong transcription	Adipose Nuclei	Adipose
44	chr17:18152800-18160000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr17:18153600-18160000	Strong transcription	Rectal Smooth Muscle	rectum
46	chr17:18153800-18160200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr17:18154200-18160000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr17:18154400-18160000	Strong transcription	Gastric	stomach
49	chr17:18156400-18160000	Strong transcription	NHDF-Ad	bronchial
50	chr17:18156800-18160200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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