Variant report

Variant	rs56089701
Chromosome Location	chr18:12704353-12704354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:12704124-12704370	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12701407..12705081-chr18:12945993..12949483,5	MCF-7	breast:
2	chr18:12696763..12699239-chr18:12701108..12704411,4	MCF-7	breast:
3	chr18:12700812..12705381-chr18:12946243..12950219,9	K562	blood:
4	chr18:12689483..12696263-chr18:12698961..12704404,9	MCF-7	breast:
5	chr18:12375314..12379217-chr18:12700733..12704866,11	K562	blood:
6	chr18:12376063..12377849-chr18:12702588..12704602,2	MCF-7	breast:
7	chr12:120729381..120730900-chr18:12702467..12704438,2	MCF-7	breast:
8	chr18:12656018..12659900-chr18:12701056..12705601,5	K562	blood:
9	chr18:12702796..12704703-chr18:12947568..12949253,2	MCF-7	breast:

No data

Variant related genes	Relation type
CEP76	TF binding region
ENSG00000085415	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000128789	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11874912	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875046	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875489	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875516	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11876168	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11877349	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12185471	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155734	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35533206	1.00[ASN][1000 genomes]
rs45460897	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55914043	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132337	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152190	1.00[ASN][1000 genomes]
rs56271712	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56359953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56382499	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56392324	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56792052	1.00[ASN][1000 genomes]
rs56909423	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58011896	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61470666	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7226376	0.86[EUR][1000 genomes]
rs7243917	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244345	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870545	1.00[ASN][1000 genomes]
rs9646473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
10	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
11	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 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	chr18:12701200-12704400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr18:12701800-12704400	Active TSS	GM12878-XiMat	blood
3	chr18:12701800-12704800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr18:12702000-12704400	Active TSS	Left Ventricle	heart
5	chr18:12703000-12704400	Active TSS	Right Atrium	heart
6	chr18:12703200-12704800	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr18:12703400-12704400	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr18:12703400-12704800	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr18:12703400-12704800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr18:12703400-12709000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr18:12703600-12704400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr18:12703600-12704400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr18:12703600-12704400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr18:12703600-12704400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr18:12703600-12704400	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr18:12703600-12704400	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr18:12703600-12704400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr18:12703600-12704400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr18:12703600-12704600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr18:12703600-12704600	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr18:12703600-12704600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr18:12703600-12704600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr18:12703600-12704600	Flanking Active TSS	Fetal Brain Female	brain
24	chr18:12703600-12704800	Flanking Active TSS	Dnd41	blood
25	chr18:12703800-12704400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
26	chr18:12703800-12704400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr18:12703800-12704400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr18:12703800-12704400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr18:12703800-12704400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr18:12703800-12704400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr18:12703800-12704400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr18:12703800-12704400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr18:12703800-12704400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr18:12703800-12704400	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr18:12703800-12704400	Flanking Active TSS	Colonic Mucosa	Colon
36	chr18:12703800-12704400	Flanking Active TSS	Fetal Brain Male	brain
37	chr18:12703800-12704400	Flanking Active TSS	Fetal Thymus	thymus
38	chr18:12703800-12704400	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr18:12703800-12704400	Flanking Active TSS	Thymus	Thymus
40	chr18:12703800-12704400	Flanking Active TSS	HUVEC	blood vessel
41	chr18:12703800-12704400	Flanking Active TSS	K562	blood
42	chr18:12703800-12704400	Flanking Active TSS	NHEK	skin
43	chr18:12703800-12704600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr18:12703800-12704800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr18:12703800-12705000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr18:12703800-12705000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr18:12703800-12705000	Flanking Active TSS	Hela-S3	cervix
48	chr18:12703800-12713200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:12704000-12704400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr18:12704000-12704400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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