Variant report

Variant	rs28464093
Chromosome Location	chr2:110309218-110309219
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	chr2:110306100..110309560-chr2:110371773..110373561,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198142	Chromatin interaction
ENSG00000186522	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10195867	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036317	1.00[ASN][1000 genomes]
rs1036318	1.00[ASN][1000 genomes]
rs10496432	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006297	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412327	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1811388	1.00[ASN][1000 genomes]
rs28553892	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570680	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28599496	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3213866	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34269507	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34311530	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34441132	1.00[ASN][1000 genomes]
rs34517320	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34821058	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35120088	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35223862	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35392016	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35531839	0.91[EUR][1000 genomes]
rs35550721	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35955221	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482487	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953721	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953729	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953730	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953788	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55794045	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56794190	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58031484	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709945	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719215	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725792	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751785	0.84[ASN][1000 genomes]
rs72824772	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72824788	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824789	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72824796	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824800	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824802	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753492	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565483	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577865	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9330317	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9330321	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750931	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9751648	0.91[EUR][1000 genomes]
rs9752531	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9798179	0.95[EUR][1000 genomes];1.00[ASN][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	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv2874	chr2:110289373-110333621	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110291000-110309400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:110291800-110309400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:110293200-110316200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:110293400-110309400	Weak transcription	Left Ventricle	heart
5	chr2:110293400-110309600	Weak transcription	Lung	lung
6	chr2:110293400-110309600	Weak transcription	NHDF-Ad	bronchial
7	chr2:110293400-110331600	Weak transcription	Right Ventricle	heart
8	chr2:110293400-110352200	Weak transcription	Gastric	stomach
9	chr2:110293600-110309400	Weak transcription	Liver	Liver
10	chr2:110296000-110312200	Weak transcription	Stomach Mucosa	stomach
11	chr2:110296400-110309400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:110296400-110309400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:110296400-110309400	Weak transcription	HSMMtube	muscle
14	chr2:110296400-110313400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:110296800-110309400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:110297400-110351600	Weak transcription	Brain Germinal Matrix	brain
17	chr2:110297800-110331800	Weak transcription	Colonic Mucosa	Colon
18	chr2:110298000-110310200	Weak transcription	Hela-S3	cervix
19	chr2:110298400-110309600	Weak transcription	Ovary	ovary
20	chr2:110299600-110309400	Weak transcription	Aorta	Aorta
21	chr2:110299600-110309600	Weak transcription	Pancreas	Pancrea
22	chr2:110299600-110318600	Weak transcription	Esophagus	oesophagus
23	chr2:110299600-110320200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:110299600-110324200	Weak transcription	Brain Angular Gyrus	brain
25	chr2:110299800-110309600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:110300200-110309400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:110300200-110309600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:110300200-110309600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:110301000-110309600	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:110301000-110310000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:110301400-110325000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:110301600-110321000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:110301800-110309600	Weak transcription	Fetal Brain Female	brain
34	chr2:110301800-110309600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:110302000-110333600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr2:110302400-110343000	Weak transcription	Psoas Muscle	Psoas
38	chr2:110303000-110320400	Weak transcription	Brain Substantia Nigra	brain
39	chr2:110303600-110309400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:110303600-110309400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:110303600-110309400	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:110303600-110309400	Weak transcription	Fetal Stomach	stomach
43	chr2:110303600-110309600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:110303600-110309600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:110303600-110309600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:110303600-110309600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:110303600-110309600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:110303600-110309600	Weak transcription	NHLF	lung
49	chr2:110303600-110309800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:110303600-110309800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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