Variant report

Variant	rs12955200
Chromosome Location	chr18:13232480-13232481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13226398..13229560-chr18:13232125..13236070,6	MCF-7	breast:
2	chr18:13217269..13219226-chr18:13231988..13233808,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168675	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12458598	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12968182	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12968748	0.88[EUR][1000 genomes]
rs3901403	0.87[EUR][1000 genomes]
rs4277409	0.87[EUR][1000 genomes]
rs4616353	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4797744	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4797747	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4797749	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4797750	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505789	0.88[EUR][1000 genomes]
rs67772629	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7228009	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7244519	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72869817	0.82[EUR][1000 genomes]
rs9944928	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9952107	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9952186	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9952516	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9952649	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9955376	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9955747	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9958724	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9962328	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9967502	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv909409	chr18:13151544-13240284	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv909410	chr18:13151544-13308950	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2182710	chr18:13232298-13232753	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv131306	chr18:13232455-13232530	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13223400-13232600	Weak transcription	Fetal Intestine Large	intestine
2	chr18:13223400-13235400	Weak transcription	Fetal Kidney	kidney
3	chr18:13223600-13235600	Weak transcription	Fetal Intestine Small	intestine
4	chr18:13223600-13241400	Weak transcription	Aorta	Aorta
5	chr18:13223800-13234200	Weak transcription	Liver	Liver
6	chr18:13223800-13259800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr18:13224000-13234800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr18:13224000-13235400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:13224000-13259800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr18:13224200-13233400	Weak transcription	HepG2	liver
11	chr18:13224400-13234000	Weak transcription	Pancreas	Pancrea
12	chr18:13224400-13234600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr18:13224400-13235400	Weak transcription	Colon Smooth Muscle	Colon
14	chr18:13224400-13235600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr18:13224400-13242600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr18:13224400-13245400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr18:13224400-13259800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr18:13225600-13232600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:13228200-13232800	Weak transcription	Esophagus	oesophagus
20	chr18:13229400-13243000	Weak transcription	Dnd41	blood
21	chr18:13229800-13233000	Weak transcription	Primary T cells from cord blood	blood
22	chr18:13230400-13232600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr18:13230400-13232600	Strong transcription	Thymus	Thymus
24	chr18:13230600-13240800	Enhancers	Fetal Brain Male	brain
25	chr18:13231000-13233000	Strong transcription	Fetal Thymus	thymus
26	chr18:13231200-13233400	Enhancers	Fetal Muscle Leg	muscle
27	chr18:13231400-13234200	Enhancers	Fetal Heart	heart
28	chr18:13231800-13233400	Enhancers	Brain Germinal Matrix	brain
29	chr18:13231800-13233600	Enhancers	Fetal Lung	lung
30	chr18:13231800-13234600	Enhancers	Left Ventricle	heart
31	chr18:13231800-13234800	Enhancers	Right Ventricle	heart
32	chr18:13232000-13232800	Enhancers	Psoas Muscle	Psoas
33	chr18:13232000-13233000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr18:13232000-13233200	Enhancers	Right Atrium	heart
35	chr18:13232000-13233600	Bivalent Enhancer	Fetal Stomach	stomach
36	chr18:13232000-13233600	Enhancers	Gastric	stomach
37	chr18:13232000-13234800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr18:13232200-13232600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr18:13232200-13232600	Enhancers	Rectal Smooth Muscle	rectum
40	chr18:13232200-13233000	Enhancers	Adipose Nuclei	Adipose
41	chr18:13232200-13233000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr18:13232200-13233000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr18:13232200-13233000	Enhancers	Spleen	Spleen
44	chr18:13232200-13233200	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr18:13232400-13232600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr18:13232400-13232600	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr18:13232400-13232600	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr18:13232400-13232600	Flanking Active TSS	Fetal Brain Female	brain
49	chr18:13232400-13233000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr18:13232400-13233000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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