Variant report

Variant	rs57620563
Chromosome Location	chr18:45458763-45458764
allele	A/C
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	POLR2A	chr18:45454367-45459190	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr18:45455632-45459226	MCF10A-Er-Src	breast:	n/a	n/a
3	RFX5	chr18:45457233-45458831	Hela-S3	cervix:	n/a	chr18:45457534-45457543 chr18:45458237-45458245 chr18:45457610-45457619
4	POLR2A	chr18:45454672-45458824	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr18:45457261-45458973	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr18:45456033-45458795	GM12891	blood:	n/a	n/a
7	POLR2A	chr18:45455468-45458915	K562	blood:	n/a	n/a
8	HCFC1	chr18:45455600-45459758	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr18:45456056-45458954	GM12878	blood:	n/a	n/a
10	POLR2A	chr18:45455888-45459386	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:45448291..45450129-chr18:45457101..45459149,2	MCF-7	breast:
2	chr18:45422809..45427886-chr18:45455832..45459212,8	MCF-7	breast:
3	chr18:45458331..45460939-chr18:45561622..45564314,2	K562	blood:
4	chr18:45457936..45459581-chr18:45522909..45525211,2	K562	blood:
5	chr18:45457637..45459201-chr18:45523865..45526054,2	MCF-7	breast:
6	chr18:45423054..45427118-chr18:45456865..45459520,4	MCF-7	breast:

Variant related genes	Relation type
SMAD2	TF binding region
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10445485	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10502890	0.99[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11082641	0.89[AFR][1000 genomes]
rs11659463	0.85[AFR][1000 genomes]
rs12457664	0.99[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12458238	0.93[AFR][1000 genomes]
rs12968493	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12969725	0.96[AFR][1000 genomes]
rs1573362	0.99[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787196	0.80[AFR][1000 genomes]
rs1787198	0.95[AFR][1000 genomes]
rs1787199	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1792667	0.95[AFR][1000 genomes]
rs1792668	0.95[AFR][1000 genomes]
rs1792674	0.91[AFR][1000 genomes]
rs1792687	0.95[AFR][1000 genomes]
rs1942158	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4940102	0.98[ASN][1000 genomes]
rs948602	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909614	chr18:45419421-45478490	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv909615	chr18:45452321-45493026	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3446751	chr18:45455904-45459152	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45457800-45458800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr18:45457800-45458800	Flanking Active TSS	Thymus	Thymus
3	chr18:45457800-45458800	Flanking Active TSS	Hela-S3	cervix
4	chr18:45457800-45458800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr18:45457800-45459000	Flanking Active TSS	Dnd41	blood
6	chr18:45458000-45458800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr18:45458000-45458800	Enhancers	Fetal Heart	heart
8	chr18:45458000-45458800	Flanking Active TSS	Stomach Mucosa	stomach
9	chr18:45458200-45458800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr18:45458200-45458800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr18:45458200-45458800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr18:45458200-45458800	Enhancers	Placenta	Placenta
13	chr18:45458200-45463400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr18:45458400-45458800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr18:45458400-45458800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr18:45458400-45458800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr18:45458400-45458800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr18:45458400-45458800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr18:45458400-45458800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr18:45458400-45458800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr18:45458400-45458800	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr18:45458400-45458800	Enhancers	Fetal Lung	lung
23	chr18:45458400-45458800	Enhancers	Fetal Muscle Leg	muscle
24	chr18:45458400-45459000	Enhancers	Primary B cells from peripheral blood	blood
25	chr18:45458400-45459000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr18:45458400-45459000	Enhancers	Pancreas	Pancrea
27	chr18:45458400-45459200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:45458400-45459200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr18:45458400-45459200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr18:45458400-45459400	Weak transcription	Gastric	stomach
31	chr18:45458400-45459600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr18:45458400-45459800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr18:45458400-45459800	Weak transcription	Spleen	Spleen
34	chr18:45458400-45461000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr18:45458400-45461800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr18:45458400-45463200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr18:45458400-45463400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr18:45458600-45458800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr18:45458600-45458800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr18:45458600-45458800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr18:45458600-45458800	Enhancers	Brain Substantia Nigra	brain
42	chr18:45458600-45458800	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr18:45458600-45458800	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr18:45458600-45458800	Active TSS	GM12878-XiMat	blood
45	chr18:45458600-45459000	Enhancers	Primary T cells from cord blood	blood
46	chr18:45458600-45459000	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr18:45458600-45459000	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr18:45458600-45459200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr18:45458600-45459200	Active TSS	Fetal Brain Male	brain
50	chr18:45458600-45459400	Enhancers	H9 Cell Line	embryonic stem cell

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