Variant report

Variant	rs9961556
Chromosome Location	chr18:12640499-12640500
allele	A/G
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	FOS	chr18:12640299-12640919	MCF10A-Er-Src	breast:	n/a	chr18:12640775-12640786
2	FOXA1	chr18:12640275-12640913	HepG2	liver:	n/a	n/a
3	MAX	chr18:12640262-12641180	A549	lung:	n/a	n/a
4	MAFK	chr18:12640026-12640921	IMR90	lung:	n/a	chr18:12640154-12640169
5	CEBPB	chr18:12640341-12640902	IMR90	lung:	n/a	n/a
6	TCF12	chr18:12640478-12641100	SK-N-SH	brain:	n/a	n/a
7	NR3C1	chr18:12640495-12640965	A549	lung:	n/a	n/a
8	JUND	chr18:12640394-12640661	HepG2	liver:	n/a	n/a
9	FOSL2	chr18:12640318-12640957	HepG2	liver:	n/a	n/a
10	POLR2A	chr18:12640322-12641050	A549	lung:	n/a	n/a
11	MAFK	chr18:12640045-12640635	Hela-S3	cervix:	n/a	chr18:12640154-12640169
12	CEBPB	chr18:12640351-12640656	HepG2	liver:	n/a	n/a
13	MAX	chr18:12640407-12641043	A549	lung:	n/a	n/a
14	MYC	chr18:12640452-12640922	MCF10A-Er-Src	breast:	n/a	n/a
15	FOSL2	chr18:12640343-12640966	MCF-7	breast:	n/a	n/a
16	MYBL2	chr18:12640341-12640960	HepG2	liver:	n/a	n/a
17	TCF12	chr18:12640173-12641064	A549	lung:	n/a	n/a
18	FOS	chr18:12640136-12640983	MCF10A-Er-Src	breast:	n/a	chr18:12640775-12640786
19	FOSL2	chr18:12640241-12641037	A549	lung:	n/a	n/a
20	TCF12	chr18:12640412-12641215	SK-N-SH	brain:	n/a	n/a
21	FOXA1	chr18:12640233-12640914	A549	lung:	n/a	n/a
22	STAT3	chr18:12640332-12640874	MCF10A-Er-Src	breast:	n/a	n/a
23	E2F4	chr18:12640147-12640908	MCF10A-Er-Src	breast:	n/a	n/a
24	EP300	chr18:12640295-12640859	HepG2	liver:	n/a	n/a
25	FOXA1	chr18:12640213-12640746	HepG2	liver:	n/a	n/a
26	NR3C1	chr18:12640268-12640957	A549	lung:	n/a	n/a
27	E2F6	chr18:12640454-12641041	A549	lung:	n/a	n/a
28	FOS	chr18:12640337-12640928	MCF10A-Er-Src	breast:	n/a	chr18:12640775-12640786
29	CEBPB	chr18:12640236-12640931	A549	lung:	n/a	n/a
30	MYC	chr18:12640471-12641128	MCF10A-Er-Src	breast:	n/a	n/a
31	MAFK	chr18:12640027-12640545	K562	blood:	n/a	chr18:12640154-12640169
32	ARID3A	chr18:12640325-12640973	HepG2	liver:	n/a	n/a
33	FOXA1	chr18:12640308-12640739	HepG2	liver:	n/a	n/a
34	FOXA2	chr18:12640300-12640609	HepG2	liver:	n/a	n/a
35	EP300	chr18:12640485-12640916	HepG2	liver:	n/a	n/a
36	FOXA1	chr18:12640290-12640644	HepG2	liver:	n/a	n/a
37	MAFK	chr18:12640027-12640503	HepG2	liver:	n/a	chr18:12640154-12640169
38	FOXA1	chr18:12640288-12640722	A549	lung:	n/a	n/a
39	SP1	chr18:12640229-12641027	A549	lung:	n/a	n/a
40	FOS	chr18:12640370-12641006	HUVEC	blood vessel:	n/a	chr18:12640775-12640786
41	POLR2A	chr18:12640261-12641081	HUVEC	blood vessel:	n/a	n/a
42	MYC	chr18:12640486-12641093	K562	blood:	n/a	n/a
43	KAP1	chr18:12640184-12641021	U2OS	brain:	n/a	n/a
44	GABPA	chr18:12640311-12640969	A549	lung:	n/a	n/a
45	CEBPB	chr18:12640337-12640996	A549	lung:	n/a	n/a
46	STAT3	chr18:12640163-12640922	MCF10A-Er-Src	breast:	n/a	n/a
47	JUN	chr18:12640347-12640942	HepG2	liver:	n/a	n/a
48	STAT3	chr18:12640343-12640877	MCF10A-Er-Src	breast:	n/a	n/a
49	CEBPB	chr18:12640412-12640735	MCF-7	breast:	n/a	n/a
50	SP1	chr18:12640276-12640928	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12639049..12640550-chr18:12644978..12647859,2	MCF-7	breast:
2	chr18:12638057..12640696-chr18:12655974..12658734,3	MCF-7	breast:
3	chr18:12639720..12643637-chr18:12655833..12659154,6	MCF-7	breast:

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

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs28411962	1.00[AMR][1000 genomes]
rs28504345	1.00[AMR][1000 genomes]
rs28533061	1.00[AMR][1000 genomes]
rs28557018	1.00[AMR][1000 genomes]
rs28599545	1.00[AMR][1000 genomes]
rs28603194	1.00[AMR][1000 genomes]
rs28608782	1.00[AMR][1000 genomes]
rs28734798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8084860	1.00[YRI][hapmap]
rs9945568	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9946958	1.00[AMR][1000 genomes]
rs9947177	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9947285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9949203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9950017	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9950999	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9951661	1.00[YRI][hapmap]
rs9953587	1.00[AMR][1000 genomes]
rs9954340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9957046	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9958917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9960826	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9961389	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9961477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12607800-12651800	Weak transcription	Brain Germinal Matrix	brain
2	chr18:12616400-12644800	Weak transcription	Brain Hippocampus Middle	brain
3	chr18:12616600-12645200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:12621200-12645200	Weak transcription	Fetal Muscle Leg	muscle
5	chr18:12622800-12645000	Weak transcription	Brain Angular Gyrus	brain
6	chr18:12626600-12640600	Weak transcription	Lung	lung
7	chr18:12630400-12645400	Weak transcription	Ovary	ovary
8	chr18:12630800-12640600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr18:12631000-12645200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr18:12631000-12645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr18:12631200-12647800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr18:12631400-12645200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr18:12633600-12655800	Weak transcription	Fetal Stomach	stomach
14	chr18:12635000-12645800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr18:12635200-12640600	Weak transcription	Gastric	stomach
16	chr18:12635200-12645800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:12637200-12641200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr18:12637600-12641200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr18:12637800-12643400	Weak transcription	Psoas Muscle	Psoas
20	chr18:12637800-12645400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr18:12637800-12652000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr18:12638000-12640800	Weak transcription	Right Ventricle	heart
23	chr18:12638400-12640600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr18:12638400-12642200	Weak transcription	Left Ventricle	heart
25	chr18:12638600-12643200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr18:12638800-12645000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr18:12638800-12645200	Weak transcription	Brain Anterior Caudate	brain
28	chr18:12639000-12641000	Enhancers	K562	blood
29	chr18:12639000-12644800	Weak transcription	Fetal Brain Female	brain
30	chr18:12639000-12645200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr18:12639400-12641200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr18:12639600-12645800	Weak transcription	Esophagus	oesophagus
33	chr18:12639800-12640600	Enhancers	HMEC	breast
34	chr18:12640000-12640800	Enhancers	Liver	Liver
35	chr18:12640000-12641200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr18:12640000-12641200	Flanking Active TSS	A549	lung
37	chr18:12640000-12641400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr18:12640200-12640800	Enhancers	HSMM	muscle
39	chr18:12640200-12641000	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr18:12640200-12641000	Enhancers	Fetal Heart	heart
41	chr18:12640200-12641200	Enhancers	NH-A	brain
42	chr18:12640200-12641200	Enhancers	NHDF-Ad	bronchial
43	chr18:12640200-12641200	Enhancers	NHLF	lung
44	chr18:12640400-12640600	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr18:12640400-12640600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr18:12640400-12640600	Enhancers	Colon Smooth Muscle	Colon
47	chr18:12640400-12640600	Enhancers	HSMMtube	muscle
48	chr18:12640400-12640600	Flanking Active TSS	HUVEC	blood vessel
49	chr18:12640400-12640800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr18:12640400-12640800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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