Variant report

Variant	rs28374561
Chromosome Location	chr2:110325040-110325041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs28361394	0.87[AFR][1000 genomes]
rs28581222	0.91[AFR][1000 genomes]
rs28603269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639612	1.00[ASW][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28658552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28707057	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28718793	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28721931	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60978762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61054424	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938243	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938247	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938294	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940226	1.00[AMR][1000 genomes]
rs7593495	1.00[CHD][hapmap]
rs9653605	0.91[AFR][1000 genomes]
rs9751748	0.82[ASW][hapmap]

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:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110293400-110331600	Weak transcription	Right Ventricle	heart
2	chr2:110293400-110352200	Weak transcription	Gastric	stomach
3	chr2:110297400-110351600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:110297800-110331800	Weak transcription	Colonic Mucosa	Colon
5	chr2:110302000-110333600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:110302400-110343000	Weak transcription	Psoas Muscle	Psoas
8	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
10	chr2:110309000-110347400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
12	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
13	chr2:110310400-110337800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:110310400-110338400	Weak transcription	Lung	lung
15	chr2:110310400-110342000	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
18	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:110310600-110341400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:110310800-110336800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:110312200-110326000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:110312200-110328400	Weak transcription	Ovary	ovary
24	chr2:110313400-110325200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:110313400-110337000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:110317000-110326800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr2:110318200-110325400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:110318200-110338000	Weak transcription	NHEK	skin
29	chr2:110318200-110348400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:110318800-110328200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:110319200-110367400	Weak transcription	HSMMtube	muscle
32	chr2:110319400-110358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:110319600-110325600	Strong transcription	Liver	Liver
34	chr2:110319800-110325800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr2:110320000-110326000	Strong transcription	HepG2	liver
36	chr2:110320200-110325400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:110320200-110325600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:110320200-110326200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:110320400-110325400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:110320600-110354600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:110320800-110325400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:110321000-110325200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:110321000-110325200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:110321200-110328400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:110321200-110332800	Weak transcription	Fetal Heart	heart
46	chr2:110321600-110325200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:110321800-110325200	Strong transcription	HSMM	muscle
48	chr2:110321800-110328400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:110322400-110328400	Weak transcription	NHLF	lung
50	chr2:110322600-110325200	Strong transcription	Osteobl	bone

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