Variant report

Variant	rs487139
Chromosome Location	chr18:12415885-12415886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXP2	chr18:12415866-12416261	SK-N-MC	brain:	n/a	n/a
2	MAX	chr18:12415667-12416051	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr18:12415564-12416192	Hela-S3	cervix:	n/a	n/a
4	MAX	chr18:12415757-12416063	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr18:12415652-12416069	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr18:12415766-12416104	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr18:12415451-12416618	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr18:12415849-12415919	HUVEC	blood vessel:	n/a	n/a
9	MAX	chr18:12415837-12416006	HepG2	liver:	n/a	n/a
10	POLR2A	chr18:12415594-12416217	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr18:12415625-12416298	SK-N-MC	brain:	n/a	n/a
12	MAX	chr18:12415676-12416112	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12407594..12413164-chr18:12414407..12422412,12	MCF-7	breast:
2	chr18:12375250..12378013-chr18:12414688..12417638,3	MCF-7	breast:

No data

Variant related genes	Relation type
SLMO1	TF binding region
ENSG00000141391	Chromatin interaction
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16977182	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16977185	0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1785658	0.80[ASN][1000 genomes]
rs2096847	0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
9	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
10	nsv909404	chr18:12409955-12438402	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr18:12408600-12419600	Weak transcription	Thymus	Thymus
2	chr18:12408800-12417800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:12408800-12419800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr18:12408800-12419800	Weak transcription	Pancreas	Pancrea
5	chr18:12409000-12416000	Weak transcription	Aorta	Aorta
6	chr18:12409000-12416000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr18:12409000-12417600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr18:12409000-12419600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr18:12409000-12419800	Weak transcription	Colonic Mucosa	Colon
10	chr18:12409000-12419800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr18:12409000-12419800	Weak transcription	Fetal Kidney	kidney
12	chr18:12409000-12419800	Weak transcription	Fetal Thymus	thymus
13	chr18:12409200-12418400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr18:12409800-12418000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr18:12409800-12419800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr18:12410200-12419800	Weak transcription	NH-A	brain
17	chr18:12410400-12417200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr18:12410400-12419800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr18:12410400-12419800	Weak transcription	Right Ventricle	heart
20	chr18:12410400-12430400	Weak transcription	A549	lung
21	chr18:12410600-12417600	Weak transcription	HMEC	breast
22	chr18:12411800-12419800	Weak transcription	NHEK	skin
23	chr18:12413800-12416600	Enhancers	Brain Hippocampus Middle	brain
24	chr18:12414000-12416200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr18:12414000-12416600	Enhancers	Brain Cingulate Gyrus	brain
26	chr18:12414200-12416400	Enhancers	Brain Angular Gyrus	brain
27	chr18:12414200-12416600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr18:12414400-12419600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:12414800-12416200	Enhancers	Spleen	Spleen
30	chr18:12414800-12416400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr18:12414800-12416600	Enhancers	Placenta	Placenta
32	chr18:12415000-12416200	Enhancers	Ovary	ovary
33	chr18:12415000-12416400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr18:12415000-12416400	Enhancers	Brain Anterior Caudate	brain
35	chr18:12415000-12416400	Enhancers	NHDF-Ad	bronchial
36	chr18:12415000-12416600	Enhancers	Fetal Muscle Leg	muscle
37	chr18:12415400-12416400	Enhancers	Fetal Brain Male	brain
38	chr18:12415400-12416400	Enhancers	HSMM	muscle
39	chr18:12415600-12416000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr18:12415600-12416000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:12415600-12416000	Enhancers	Esophagus	oesophagus
42	chr18:12415600-12416000	Flanking Active TSS	HepG2	liver
43	chr18:12415600-12416000	Enhancers	NHLF	lung
44	chr18:12415600-12416200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr18:12415600-12416200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr18:12415600-12416200	Enhancers	H9 Cell Line	embryonic stem cell
47	chr18:12415600-12416200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr18:12415600-12416200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr18:12415600-12416200	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr18:12415600-12416200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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