Variant report

Variant	rs28563139
Chromosome Location	chr18:13280480-13280481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13276824..13278718-chr18:13280381..13284195,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168675	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10775420	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10853230	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11080640	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11080641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11662800	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12457309	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56078702	0.83[ASN][1000 genomes]
rs7228720	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7232054	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8093127	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv2209	chr18:13276410-13316570	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13261200-13282200	Weak transcription	Small Intestine	intestine
2	chr18:13270000-13283800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr18:13270000-13290000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr18:13270200-13284600	Weak transcription	Psoas Muscle	Psoas
5	chr18:13270200-13288200	Weak transcription	Fetal Intestine Large	intestine
6	chr18:13270200-13290200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr18:13270200-13297600	Weak transcription	Colonic Mucosa	Colon
8	chr18:13270800-13282600	Weak transcription	Fetal Intestine Small	intestine
9	chr18:13271400-13281600	Weak transcription	Brain Germinal Matrix	brain
10	chr18:13272800-13284800	Weak transcription	Esophagus	oesophagus
11	chr18:13272800-13289600	Weak transcription	Gastric	stomach
12	chr18:13273200-13283800	Weak transcription	Spleen	Spleen
13	chr18:13274600-13282400	Weak transcription	HepG2	liver
14	chr18:13274600-13284000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr18:13274600-13284200	Weak transcription	Colon Smooth Muscle	Colon
16	chr18:13274600-13301600	Weak transcription	Brain Substantia Nigra	brain
17	chr18:13274600-13302400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr18:13276400-13281200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr18:13277400-13280600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr18:13277400-13281600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr18:13277400-13284600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr18:13277600-13281800	Strong transcription	Thymus	Thymus
23	chr18:13277600-13284600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr18:13277600-13284800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr18:13277800-13284800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr18:13278200-13280800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr18:13278200-13282400	Strong transcription	Fetal Stomach	stomach
28	chr18:13278200-13282800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr18:13278200-13282800	Strong transcription	Dnd41	blood
30	chr18:13278600-13280800	Strong transcription	Liver	Liver
31	chr18:13278600-13283800	Weak transcription	Aorta	Aorta
32	chr18:13278800-13280800	Enhancers	Primary B cells from peripheral blood	blood
33	chr18:13279000-13280800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr18:13279000-13280800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr18:13279000-13280800	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr18:13279000-13281000	Enhancers	Fetal Brain Male	brain
37	chr18:13279000-13281000	Enhancers	Fetal Kidney	kidney
38	chr18:13279200-13280600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr18:13279200-13281200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr18:13279400-13281000	Enhancers	HSMMtube	muscle
41	chr18:13279600-13280600	Enhancers	Brain Hippocampus Middle	brain
42	chr18:13279600-13280600	Enhancers	Fetal Brain Female	brain
43	chr18:13279600-13280800	Enhancers	Primary T cells from cord blood	blood
44	chr18:13279600-13281200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr18:13279600-13281800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr18:13279600-13283400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr18:13279600-13288600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr18:13279800-13280800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr18:13279800-13281000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr18:13279800-13281000	Enhancers	Primary T helper cells fromperipheralblood	blood

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