Variant report

Variant	rs56258053
Chromosome Location	chr18:12407581-12407582
allele	C/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	SIN3AK20	chr18:12407580-12408314	PANC-1	pancreas:	n/a	n/a
5	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
6	YY1	chr18:12407544-12408297	GM12892	blood:	n/a	chr18:12407956-12407970 chr18:12407952-12407966 chr18:12407733-12407747 chr18:12407959-12407973
7	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
8	REST	chr18:12407485-12408199	PFSK-1	brain:	n/a	chr18:12407676-12407685
9	HDAC2	chr18:12407505-12408244	MCF-7	breast:	n/a	n/a
10	TCF12	chr18:12407544-12408319	A549	lung:	n/a	n/a
11	MAX	chr18:12407530-12408876	NB4	blood:	n/a	chr18:12407992-12408002
12	REST	chr18:12407459-12407922	GM12878	blood:	n/a	chr18:12407676-12407685
13	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
14	STAT5A	chr18:12407495-12407826	GM12878	blood:	n/a	n/a
15	POLR2A	chr18:12407580-12408297	IMR90	lung:	n/a	n/a
16	PML	chr18:12407528-12408773	GM12878	blood:	n/a	n/a
17	HA-E2F1	chr18:12407528-12408213	MCF-7	breast:	n/a	chr18:12407805-12407814 chr18:12408126-12408135
18	HCFC1	chr18:12407482-12409201	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr18:12407562-12408301	SK-N-MC	brain:	n/a	n/a
20	SP1	chr18:12407494-12408323	HCT-116	colon:	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
21	MXI1	chr18:12407476-12408890	IMR90	lung:	n/a	n/a
22	ELF1	chr18:12407502-12408308	GM12878	blood:	n/a	chr18:12407947-12407959
23	E2F6	chr18:12407475-12408268	A549	lung:	n/a	chr18:12407805-12407814 chr18:12408126-12408135
24	E2F6	chr18:12407566-12408214	A549	lung:	n/a	chr18:12407805-12407814 chr18:12408126-12408135
25	SRF	chr18:12407525-12408278	MCF-7	breast:	n/a	n/a
26	MXI1	chr18:12407476-12409142	SK-N-SH	brain:	n/a	n/a
27	RUNX3	chr18:12407534-12408291	GM12878	blood:	n/a	n/a
28	SP1	chr18:12407511-12408308	HCT-116	colon:	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
29	RCOR1	chr18:12407577-12408060	K562	blood:	n/a	n/a
30	EGR1	chr18:12407502-12408208	HCT-116	colon:	n/a	chr18:12407804-12407814 chr18:12407892-12407906
31	MAX	chr18:12407509-12408778	SK-N-SH	brain:	n/a	chr18:12407992-12408002
32	CHD2	chr18:12407581-12408152	Hela-S3	cervix:	n/a	chr18:12408122-12408132
33	POLR2A	chr18:12407561-12408857	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr18:12407497-12408886	SK-N-SH	brain:	n/a	chr18:12407992-12408002
35	MAX	chr18:12407477-12408307	HCT-116	colon:	n/a	chr18:12407992-12408002
36	POLR2A	chr18:12407478-12408270	U87	brain:	n/a	n/a
37	TEAD4	chr18:12407571-12408238	K562	blood:	n/a	n/a
38	REST	chr18:12407471-12408162	PFSK-1	brain:	n/a	chr18:12407676-12407685
39	POLR2A	chr18:12407579-12408836	Hela-S3	cervix:	n/a	n/a
40	NRF1	chr18:12407553-12408494	SK-N-SH	brain:	n/a	chr18:12407959-12407973 chr18:12407805-12407814
41	ZNF263	chr18:12407568-12408210	HEK293-T-REx	kidney:	n/a	n/a
42	EGR1	chr18:12407566-12408506	HCT-116	colon:	n/a	chr18:12407804-12407814 chr18:12408306-12408320 chr18:12407892-12407906
43	E2F6	chr18:12407555-12408658	K562	blood:	n/a	chr18:12408418-12408425 chr18:12407805-12407814 chr18:12408126-12408135
44	TAF1	chr18:12407579-12408168	PFSK-1	brain:	n/a	n/a
45	EGR1	chr18:12407561-12407993	MCF-7	breast:	n/a	chr18:12407804-12407814 chr18:12407892-12407906
46	MAX	chr18:12407492-12408339	MCF-7	breast:	n/a	chr18:12407992-12408002
47	MAX	chr18:12407493-12408837	A549	lung:	n/a	chr18:12407992-12408002
48	MAX	chr18:12407525-12408171	H1-hESC	embryonic stem cell:	n/a	chr18:12407992-12408002
49	KAP1	chr18:12407553-12408039	HEK293	kidney:	n/a	n/a
50	MAX	chr18:12407497-12408424	H1-hESC	embryonic stem cell:	n/a	chr18:12407992-12408002

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr18:12407563-12407613	GM12892	blood:	n/a
2	chr18:12407563-12407613	AG04449	skin:	fetal
3	chr18:12407563-12407613	RPTEC	kidney:	n/a
4	chr18:12407563-12407613	NT2-D1	testis:	n/a
5	chr18:12407563-12407613	SAEC	small airway:	n/a
6	chr18:12407563-12407613	HRE	kidney:	n/a
7	chr18:12407563-12407613	HRPEpiC	eye:	n/a
8	chr18:12407563-12407613	NH-A	brain:	n/a
9	chr18:12407563-12407613	SK-N-SH_RA	brain:	n/a
10	chr18:12407563-12407613	AoSMC	blood vessel:	n/a
11	chr18:12407563-12407613	NHBE	bronchial:	n/a
12	chr18:12407563-12407613	HCT-116	colon:	n/a
13	chr18:12407563-12407613	A549	lung:	n/a
14	chr18:12407563-12407613	PANC-1	pancreas:	n/a
15	chr18:12407563-12407613	HPAEpiC	pulmonary alveolar:	n/a
16	chr18:12407563-12407613	HCPEpiC	choroid plexus:	n/a
17	chr18:12407563-12407613	Jurkat	blood:	n/a
18	chr18:12407563-12407613	SKMC	muscle:	n/a
19	chr18:12407563-12407613	HEK293	kidney:	embryo
20	chr18:12407563-12407613	GM12878	blood:	n/a
21	chr18:12407563-12407613	HMEC	breast:	n/a
22	chr18:12407563-12407613	IMR90	lung:	fetal
23	chr18:12407563-12407613	PrEC	prostate:	n/a
24	chr18:12407563-12407613	HEEpiC	esophagus:	n/a
25	chr18:12407563-12407613	K562	blood:	n/a
26	chr18:12407563-12407613	HIPEpiC	eye:	n/a
27	chr18:12407563-12407613	HRCEpiC	kidney:	n/a
28	chr18:12407563-12407613	MCF10A-Er-Src	breast:	n/a
29	chr18:12407563-12407613	ECC-1	luminal epithelium:	n/a
30	chr18:12407563-12407613	ovcar-3	ovarian:	n/a
31	chr18:12407563-12407613	CMK	blood:	n/a
32	chr18:12407563-12407613	Hela-S3	cervix:	n/a
33	chr18:12407563-12407613	U87	brain:	n/a
34	chr18:12407563-12407613	HCF	heart:	n/a
35	chr18:12407563-12407613	ProgFib	skin:	n/a
36	chr18:12407563-12407613	H1-hESC	embryonic stem cell:	embryo
37	chr18:12407563-12407613	MCF-7	breast:	n/a
38	chr18:12407563-12407613	SK-N-SH	brain:	n/a
39	chr18:12407563-12407613	GM19239	blood:	n/a
40	chr18:12407563-12407613	HL-60	blood:	n/a
41	chr18:12407563-12407613	GM06990	blood:	n/a
42	chr18:12407563-12407613	PFSK-1	brain:	n/a
43	chr18:12407563-12407613	HepG2	liver:	n/a
44	chr18:12407563-12407613	Hepatocyte	liver:	n/a
45	chr18:12407563-12407613	HAEpiC	amniotic membrane:	n/a
46	chr18:12407563-12407613	AG04450	lung:	fetal
47	chr18:12407563-12407613	Caco-2	colon:	n/a
48	chr18:12407563-12407613	HUVEC	blood vessel:	n/a
49	chr18:12407563-12407613	LNCaP	prostate:	n/a
50	chr18:12407563-12407613	AG09319	gingival:	n/a

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	chr18:12405095..12407603-chr18:12698505..12700605,2	K562	blood:
7	chr18:12396874..12399343-chr18:12404979..12407652,2	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
SLMO1	CpG island
ENSG00000134278	Chromatin interaction
ENSG00000141391	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000251937	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1785322	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs486922	1.00[AFR][1000 genomes]
rs510878	1.00[AMR][1000 genomes]
rs512810	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs559958	1.00[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

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12404200-12407600	Weak transcription	HSMM	muscle
2	chr18:12404400-12407600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:12404400-12407600	Weak transcription	NHLF	lung
4	chr18:12405200-12407600	Weak transcription	HSMMtube	muscle
5	chr18:12405200-12407600	Weak transcription	NHDF-Ad	bronchial
6	chr18:12406200-12407600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr18:12406400-12407600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr18:12406400-12408400	Enhancers	Fetal Brain Male	brain
9	chr18:12406400-12408600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr18:12406600-12407600	Enhancers	Primary hematopoietic stem cells	blood
11	chr18:12406600-12407600	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr18:12406600-12407600	Weak transcription	A549	lung
13	chr18:12406600-12407600	Weak transcription	HMEC	breast
14	chr18:12406800-12407600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
15	chr18:12406800-12407600	Bivalent Enhancer	Thymus	Thymus
16	chr18:12406800-12407600	Enhancers	NH-A	brain
17	chr18:12406800-12408600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr18:12407000-12407600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr18:12407000-12407600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
20	chr18:12407000-12407600	Enhancers	Esophagus	oesophagus
21	chr18:12407000-12407600	Enhancers	Pancreas	Pancrea
22	chr18:12407000-12407600	Enhancers	Spleen	Spleen
23	chr18:12407000-12407800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr18:12407000-12407800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr18:12407000-12407800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
26	chr18:12407000-12408400	Active TSS	Rectal Smooth Muscle	rectum
27	chr18:12407000-12408600	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr18:12407000-12408600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr18:12407000-12408600	Active TSS	Brain Hippocampus Middle	brain
30	chr18:12407000-12409000	Active TSS	Stomach Smooth Muscle	stomach
31	chr18:12407000-12409200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr18:12407200-12407600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr18:12407200-12407600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr18:12407200-12407800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr18:12407200-12408000	Enhancers	Fetal Lung	lung
36	chr18:12407200-12408000	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr18:12407200-12408200	Active TSS	Primary T cells from cord blood	blood
38	chr18:12407200-12408600	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr18:12407200-12408600	Active TSS	Brain Angular Gyrus	brain
40	chr18:12407200-12408600	Active TSS	Ovary	ovary
41	chr18:12407200-12408600	Active TSS	Hela-S3	cervix
42	chr18:12407200-12408600	Active TSS	Osteobl	bone
43	chr18:12407200-12409000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr18:12407200-12410000	Active TSS	Fetal Brain Female	brain
45	chr18:12407400-12407600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr18:12407400-12407600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
47	chr18:12407400-12407600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr18:12407400-12407600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr18:12407400-12407600	Enhancers	Fetal Stomach	stomach
50	chr18:12407400-12407600	Active TSS	Rectal Mucosa Donor 31	rectum

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