Variant report

Variant	rs477316
Chromosome Location	chr18:12443750-12443751
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12443233..12445110-chr18:12655911..12658418,2	MCF-7	breast:
2	chr18:12373675..12375792-chr18:12443379..12445132,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLMO1-1	chr18:12443295-12448204	ENSG00000267199.1

Variant related genes	Relation type
ENSG00000134278	Chromatin interaction
ENSG00000215527	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11080591	1.00[CEU][hapmap]
rs1652681	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3931007	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs483005	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497534	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517382	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs522631	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546932	1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554389	0.86[JPT][hapmap]
rs578667	0.86[JPT][hapmap]
rs6505759	1.00[CEU][hapmap]
rs7506835	1.00[CEU][hapmap]
rs9967267	1.00[CEU][hapmap];0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr18:12421200-12447600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr18:12421200-12452800	Weak transcription	Colonic Mucosa	Colon
4	chr18:12421400-12444200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr18:12428600-12443800	Weak transcription	HSMMtube	muscle
6	chr18:12431000-12447600	Weak transcription	NH-A	brain
7	chr18:12431000-12449200	Weak transcription	Pancreas	Pancrea
8	chr18:12431200-12447800	Weak transcription	NHEK	skin
9	chr18:12432000-12443800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr18:12432600-12447000	Weak transcription	HMEC	breast
11	chr18:12433000-12448800	Weak transcription	HUVEC	blood vessel
12	chr18:12433200-12444000	Weak transcription	Left Ventricle	heart
13	chr18:12433200-12444000	Weak transcription	Right Ventricle	heart
14	chr18:12433200-12449200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr18:12433200-12449200	Weak transcription	Gastric	stomach
16	chr18:12433200-12449200	Weak transcription	Spleen	Spleen
17	chr18:12433200-12450200	Weak transcription	Thymus	Thymus
18	chr18:12433200-12464600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr18:12433400-12458600	Weak transcription	HepG2	liver
20	chr18:12434200-12477000	Weak transcription	Esophagus	oesophagus
21	chr18:12435000-12443800	Weak transcription	Brain Hippocampus Middle	brain
22	chr18:12435000-12444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr18:12435000-12444000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr18:12435200-12444200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr18:12435200-12449000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr18:12438200-12449200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr18:12439000-12443800	Weak transcription	Brain Anterior Caudate	brain
28	chr18:12439200-12448800	Weak transcription	NHLF	lung
29	chr18:12439400-12468200	Weak transcription	K562	blood
30	chr18:12441400-12446000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr18:12441600-12452200	Weak transcription	Hela-S3	cervix
32	chr18:12441800-12443800	Weak transcription	Aorta	Aorta
33	chr18:12442000-12443800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr18:12442000-12443800	Weak transcription	Brain Substantia Nigra	brain
35	chr18:12442000-12459200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr18:12442400-12443800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr18:12443000-12444000	Strong transcription	NHDF-Ad	bronchial
38	chr18:12443000-12444600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr18:12443000-12444600	ZNF genes & repeats	Fetal Lung	lung
40	chr18:12443000-12444600	ZNF genes & repeats	Osteobl	bone
41	chr18:12443000-12445800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr18:12443000-12446000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr18:12443200-12445600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
44	chr18:12443200-12457400	Strong transcription	HSMM	muscle
45	chr18:12443400-12443800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr18:12443400-12443800	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr18:12443400-12444000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr18:12443400-12444000	Strong transcription	A549	lung
49	chr18:12443400-12444200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
50	chr18:12443400-12444200	ZNF genes & repeats	Ovary	ovary

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