Variant report

Variant	rs12967213
Chromosome Location	chr18:12407916-12407917
allele	G/T
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	REST	chr18:12407580-12408170	ECC-1	luminal epithelium:	n/a	chr18:12407676-12407685
2	MAX	chr18:12407572-12408892	Hela-S3	cervix:	n/a	chr18:12407992-12408002
3	RUNX3	chr18:12407526-12408301	GM12878	blood:	n/a	n/a
4	SP1	chr18:12407647-12408193	H1-hESC	embryonic stem cell:	n/a	chr18:12407877-12407889 chr18:12407878-12407887 chr18:12408119-12408128 chr18:12408118-12408127 chr18:12407878-12407888 chr18:12407877-12407888 chr18:12407877-12407889 chr18:12407879-12407888 chr18:12408117-12408129 chr18:12407892-12407903 chr18:12408118-12408127
5	SIN3AK20	chr18:12407580-12408314	PANC-1	pancreas:	n/a	n/a
6	EP300	chr18:12407467-12408318	ECC-1	luminal epithelium:	n/a	chr18:12407805-12407814 chr18:12407954-12407970 chr18:12408126-12408135 chr18:12408119-12408135 chr18:12408053-12408069
7	POLR2A	chr18:12407633-12408306	GM12878	blood:	n/a	n/a
8	MYC	chr18:12407652-12408369	MCF-7	breast:	n/a	chr18:12407992-12408002
9	YY1	chr18:12407544-12408297	GM12892	blood:	n/a	chr18:12407956-12407970 chr18:12407952-12407966 chr18:12407733-12407747 chr18:12407959-12407973
10	YY1	chr18:12407716-12408107	K562	blood:	n/a	chr18:12407956-12407970 chr18:12407952-12407966 chr18:12407733-12407747 chr18:12407959-12407973
11	MEF2A	chr18:12407504-12408036	GM12878	blood:	n/a	chr18:12407814-12407835 chr18:12407814-12407835 chr18:12407814-12407835 chr18:12407815-12407830 chr18:12407816-12407830 chr18:12407819-12407828 chr18:12407815-12407830 chr18:12407816-12407831 chr18:12407818-12407829 chr18:12407815-12407831 chr18:12407815-12407830 chr18:12407817-12407828
12	ELF1	chr18:12407684-12408320	K562	blood:	n/a	chr18:12407947-12407959
13	CHD2	chr18:12407650-12408190	K562	blood:	n/a	chr18:12408122-12408132
14	REST	chr18:12407485-12408199	PFSK-1	brain:	n/a	chr18:12407676-12407685
15	PAX5	chr18:12407761-12408109	GM12878	blood:	n/a	n/a
16	MYC	chr18:12407721-12408915	MCF10A-Er-Src	breast:	n/a	chr18:12407992-12408002
17	TBL1XR1	chr18:12407586-12408111	K562	blood:	n/a	n/a
18	POLR2A	chr18:12407596-12408262	Hela-S3	cervix:	n/a	n/a
19	MAZ	chr18:12407609-12408231	Hela-S3	cervix:	n/a	n/a
20	TBP	chr18:12407621-12408097	Hela-S3	cervix:	n/a	n/a
21	UBTF	chr18:12407656-12408857	K562	blood:	n/a	n/a
22	YY1	chr18:12407867-12408092	A549	lung:	n/a	chr18:12407956-12407970 chr18:12407952-12407966 chr18:12407959-12407973
23	HDAC2	chr18:12407505-12408244	MCF-7	breast:	n/a	n/a
24	TCF12	chr18:12407544-12408319	A549	lung:	n/a	n/a
25	TAF1	chr18:12407844-12408098	GM12891	blood:	n/a	n/a
26	YY1	chr18:12407779-12408168	SK-N-SH_RA	brain:	n/a	chr18:12407956-12407970 chr18:12407952-12407966 chr18:12407959-12407973
27	MAX	chr18:12407530-12408876	NB4	blood:	n/a	chr18:12407992-12408002
28	POLR2A	chr18:12407759-12408140	SK-N-MC	brain:	n/a	n/a
29	YY1	chr18:12407750-12408107	SK-N-SH_RA	brain:	n/a	chr18:12407956-12407970 chr18:12407952-12407966 chr18:12407959-12407973
30	USF1	chr18:12407805-12408123	SK-N-SH_RA	brain:	n/a	n/a
31	NFYB	chr18:12407779-12407979	GM12878	blood:	n/a	n/a
32	REST	chr18:12407459-12407922	GM12878	blood:	n/a	chr18:12407676-12407685
33	HEY1	chr18:12407815-12408197	K562	blood:	n/a	n/a
34	ZNF143	chr18:12407608-12407963	K562	blood:	n/a	chr18:12407804-12407814
35	POLR2A	chr18:12407617-12408302	A549	lung:	n/a	n/a
36	USF2	chr18:12407731-12408121	GM12878	blood:	n/a	n/a
37	SP1	chr18:12407611-12408285	K562	blood:	n/a	chr18:12407877-12407889 chr18:12407878-12407887 chr18:12408119-12408128 chr18:12408118-12408127 chr18:12407878-12407888 chr18:12407877-12407888 chr18:12407877-12407889 chr18:12407879-12407888 chr18:12408117-12408129 chr18:12407892-12407903 chr18:12408118-12408127
38	MYC	chr18:12407641-12408251	MCF-7	breast:	n/a	chr18:12407992-12408002
39	POLR2A	chr18:12407749-12408144	K562	blood:	n/a	n/a
40	PML	chr18:12407842-12408063	GM12878	blood:	n/a	n/a
41	CHD1	chr18:12407898-12408120	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAL1	chr18:12407653-12408175	K562	blood:	n/a	n/a
43	IRF1	chr18:12407665-12408129	K562	blood:	n/a	chr18:12407875-12407889
44	NFIC	chr18:12407829-12408181	GM12878	blood:	n/a	n/a
45	TAF1	chr18:12407708-12408156	PFSK-1	brain:	n/a	n/a
46	IRF1	chr18:12407647-12408075	K562	blood:	n/a	chr18:12407875-12407889
47	POLR2A	chr18:12407705-12408197	HCT-116	colon:	n/a	n/a
48	POLR2A	chr18:12407649-12408310	K562	blood:	n/a	n/a
49	USF1	chr18:12407605-12408194	ECC-1	luminal epithelium:	n/a	n/a
50	MEF2A	chr18:12407432-12408091	SK-N-SH	brain:	n/a	chr18:12407814-12407835 chr18:12407814-12407835 chr18:12407814-12407835 chr18:12407815-12407830 chr18:12407816-12407830 chr18:12407819-12407828 chr18:12407815-12407830 chr18:12407816-12407831 chr18:12407818-12407829 chr18:12407815-12407831 chr18:12407815-12407830 chr18:12407817-12407828

No.	Distal block	Cell Line	Cell type
1	chr18:12375996..12378292-chr18:12406153..12409059,2	MCF-7	breast:
2	chr18:12406749..12409861-chr18:12418820..12421803,8	MCF-7	breast:
3	chr18:12374593..12378692-chr18:12406477..12410976,5	K562	blood:
4	chr18:12404079..12409500-chr18:12655702..12659746,9	K562	blood:
5	chr18:12406252..12409116-chr18:12699672..12701773,2	MCF-7	breast:
6	chr11:71823348..71823895-chr18:12407725..12408414,2	Hela-S3	cervix:
7	chr18:12407594..12413164-chr18:12414407..12422412,12	MCF-7	breast:
8	chr18:12375261..12378325-chr18:12405563..12409497,4	MCF-7	breast:
9	chr18:12395807..12401661-chr18:12404688..12409428,6	K562	blood:
10	chr18:12406559..12410304-chr18:12656888..12659730,4	MCF-7	breast:

Variant related genes	Relation type
SLMO1	TF binding region
ENSG00000134278	Chromatin interaction
ENSG00000251937	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000141391	Chromatin interaction
ENSG00000110200	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10164125	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11080575	0.81[AMR][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	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv1060728	chr18:12364077-12410409	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv978720	chr18:12395653-12408191	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	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
11	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12967213	SLMO1	cis	Esophagus Muscularis	GTEx
rs12967213	AP001029.1	cis	Esophagus Muscularis	GTEx
rs12967213	TUBB6	cis	Whole Blood	GTEx
rs12967213	SLMO1	cis	Artery Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12406400-12408400	Enhancers	Fetal Brain Male	brain
2	chr18:12406400-12408600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr18:12406800-12408600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:12407000-12408400	Active TSS	Rectal Smooth Muscle	rectum
5	chr18:12407000-12408600	Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr18:12407000-12408600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:12407000-12408600	Active TSS	Brain Hippocampus Middle	brain
8	chr18:12407000-12409000	Active TSS	Stomach Smooth Muscle	stomach
9	chr18:12407000-12409200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr18:12407200-12408000	Enhancers	Fetal Lung	lung
11	chr18:12407200-12408000	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr18:12407200-12408200	Active TSS	Primary T cells from cord blood	blood
13	chr18:12407200-12408600	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr18:12407200-12408600	Active TSS	Brain Angular Gyrus	brain
15	chr18:12407200-12408600	Active TSS	Ovary	ovary
16	chr18:12407200-12408600	Active TSS	Hela-S3	cervix
17	chr18:12407200-12408600	Active TSS	Osteobl	bone
18	chr18:12407200-12409000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr18:12407200-12410000	Active TSS	Fetal Brain Female	brain
20	chr18:12407400-12408000	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr18:12407400-12408000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr18:12407400-12408400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr18:12407400-12408400	Active TSS	Muscle Satellite Cultured Cells	--
24	chr18:12407400-12408400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr18:12407400-12408400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr18:12407400-12408400	Active TSS	Adipose Nuclei	Adipose
27	chr18:12407400-12408600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:12407400-12408600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr18:12407400-12408600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr18:12407400-12408600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr18:12407400-12408600	Active TSS	Brain Anterior Caudate	brain
32	chr18:12407400-12408600	Active TSS	Brain Cingulate Gyrus	brain
33	chr18:12407400-12408600	Active TSS	Colon Smooth Muscle	Colon
34	chr18:12407400-12408600	Active TSS	Fetal Kidney	kidney
35	chr18:12407400-12408600	Active TSS	Right Ventricle	heart
36	chr18:12407400-12408800	Active TSS	Brain Germinal Matrix	brain
37	chr18:12407400-12408800	Active TSS	Brain Substantia Nigra	brain
38	chr18:12407400-12409000	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr18:12407400-12409000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr18:12407400-12409000	Active TSS	Duodenum Mucosa	Duodenum
41	chr18:12407600-12408000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr18:12407600-12408000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
43	chr18:12407600-12408200	Active TSS	Spleen	Spleen
44	chr18:12407600-12408400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr18:12407600-12408400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr18:12407600-12408600	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr18:12407600-12408600	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr18:12407600-12408600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
49	chr18:12407600-12408600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr18:12407600-12408600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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