Variant report

Variant	rs73407558
Chromosome Location	chr18:12653324-12653325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr18:12652991-12653369	SH-SY5Y	brain:	n/a	n/a
2	MAFK	chr18:12653062-12653416	HepG2	liver:	n/a	n/a
3	USF2	chr18:12653003-12653359	Hela-S3	cervix:	n/a	n/a
4	FOS	chr18:12653054-12653412	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA3	chr18:12652756-12653720	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr18:12652706-12653772	SK-N-SH	brain:	n/a	n/a
7	EP300	chr18:12653014-12653434	SK-N-SH_RA	brain:	n/a	n/a
8	FOS	chr18:12652872-12653380	MCF10A-Er-Src	breast:	n/a	n/a
9	RCOR1	chr18:12652984-12653386	K562	blood:	n/a	n/a
10	CEBPB	chr18:12652976-12653400	IMR90	lung:	n/a	n/a
11	MAFK	chr18:12653066-12653406	HepG2	liver:	n/a	n/a
12	TCF7L2	chr18:12653024-12653392	Hela-S3	cervix:	n/a	n/a
13	RXRA	chr18:12652908-12653589	SK-N-SH	brain:	n/a	n/a
14	PBX3	chr18:12652892-12653699	SK-N-SH	brain:	n/a	n/a
15	FOS	chr18:12653057-12653412	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr18:12653141-12653340	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr18:12653151-12653351	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr18:12653238-12653403	MCF10A-Er-Src	breast:	n/a	n/a
19	GATA3	chr18:12652880-12653759	SK-N-SH	brain:	n/a	n/a
20	NFIC	chr18:12652887-12653615	SK-N-SH	brain:	n/a	n/a
21	RAD21	chr18:12652860-12653351	Hela-S3	cervix:	n/a	n/a
22	RCOR1	chr18:12652960-12653356	Hela-S3	cervix:	n/a	n/a
23	TEAD4	chr18:12652897-12653581	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr18:12653006-12653632	SK-N-SH	brain:	n/a	n/a
25	EP300	chr18:12652901-12653404	Hela-S3	cervix:	n/a	n/a
26	EP300	chr18:12652970-12653459	SK-N-SH_RA	brain:	n/a	n/a
27	SMC3	chr18:12652887-12653378	Hela-S3	cervix:	n/a	n/a
28	MAFK	chr18:12653017-12653420	IMR90	lung:	n/a	n/a
29	PBX3	chr18:12652875-12653567	SK-N-SH	brain:	n/a	n/a
30	EP300	chr18:12652848-12653573	SK-N-SH	brain:	n/a	n/a
31	REST	chr18:12652959-12653326	PFSK-1	brain:	n/a	n/a
32	EP300	chr18:12652917-12653393	K562	blood:	n/a	n/a
33	TCF12	chr18:12652707-12653819	SK-N-SH	brain:	n/a	n/a
34	CEBPB	chr18:12652923-12653398	Hela-S3	cervix:	n/a	n/a
35	ARID3A	chr18:12652724-12653356	K562	blood:	n/a	n/a
36	MAFF	chr18:12653087-12653410	HepG2	liver:	n/a	n/a
37	SIN3AK20	chr18:12653029-12653360	SK-N-SH	brain:	n/a	n/a
38	MAFK	chr18:12652998-12653378	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12648702..12654959-chr18:12655130..12658770,8	K562	blood:
2	chr18:12643422..12646156-chr18:12653146..12655533,3	MCF-7	breast:
3	chr18:12649857..12654959-chr18:12655130..12658770,11	K562	blood:
4	chr18:12651259..12653780-chr18:12656567..12658681,4	MCF-7	breast:

No data

Variant related genes	Relation type
SPIRE1	TF binding region
ENSG00000215527	TF binding region
ENSG00000215527	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000128789	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs4313868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58991139	1.00[AMR][1000 genomes]
rs73403718	1.00[AMR][1000 genomes]
rs73403736	1.00[AMR][1000 genomes]
rs73403739	1.00[AMR][1000 genomes]
rs73403744	1.00[AMR][1000 genomes]
rs73405595	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73407539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73407559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73407561	1.00[AMR][1000 genomes]
rs73407562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73407563	1.00[AFR][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	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	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv3397790	chr18:12649001-12673755	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv576497	chr18:12650900-12658293	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv576498	chr18:12650900-12658436	Weak transcription Enhancers Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12633600-12655800	Weak transcription	Fetal Stomach	stomach
2	chr18:12646000-12654000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr18:12646200-12657000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr18:12646200-12657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:12646400-12656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr18:12646400-12656600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:12646400-12657000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:12648000-12656800	Weak transcription	Left Ventricle	heart
9	chr18:12648400-12656600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:12648600-12655800	Weak transcription	Fetal Muscle Leg	muscle
11	chr18:12648600-12656800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr18:12650000-12654400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr18:12651000-12653400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr18:12651000-12653600	Enhancers	Brain Substantia Nigra	brain
15	chr18:12651000-12654000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr18:12651200-12653600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr18:12651200-12653600	Enhancers	Fetal Heart	heart
18	chr18:12651400-12653800	Enhancers	Brain Cingulate Gyrus	brain
19	chr18:12651600-12653400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr18:12651600-12653400	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr18:12651600-12653600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:12651600-12653600	Enhancers	HSMM	muscle
23	chr18:12651800-12653400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr18:12651800-12653600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr18:12651800-12653600	Enhancers	Brain Germinal Matrix	brain
26	chr18:12651800-12653600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr18:12651800-12654000	Enhancers	Brain Hippocampus Middle	brain
28	chr18:12652000-12653400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr18:12652000-12653600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr18:12652000-12653600	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr18:12652200-12653600	Flanking Active TSS	Fetal Brain Female	brain
32	chr18:12652200-12653600	Enhancers	NH-A	brain
33	chr18:12652200-12655400	Enhancers	Fetal Brain Male	brain
34	chr18:12652400-12653600	Enhancers	Brain Angular Gyrus	brain
35	chr18:12652400-12654000	Enhancers	Adipose Nuclei	Adipose
36	chr18:12652400-12654000	Enhancers	HUVEC	blood vessel
37	chr18:12652600-12653400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr18:12652600-12653400	Enhancers	HMEC	breast
39	chr18:12652600-12653600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr18:12652600-12654000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr18:12652600-12655400	Weak transcription	Fetal Kidney	kidney
42	chr18:12652800-12653400	Enhancers	H1 Cell Line	embryonic stem cell
43	chr18:12652800-12653600	Enhancers	Brain Anterior Caudate	brain
44	chr18:12652800-12653600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr18:12652800-12653800	Enhancers	Ovary	ovary
46	chr18:12652800-12653800	Enhancers	K562	blood
47	chr18:12652800-12654200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr18:12653000-12653400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr18:12653000-12653400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr18:12653000-12653400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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