Variant report

Variant	rs28639612
Chromosome Location	chr2:110348339-110348340
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	chr2:110337969..110339732-chr2:110347344..110349136,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs28361394	0.87[AFR][1000 genomes]
rs28374561	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]
rs28576601	0.83[YRI][hapmap]
rs28581222	0.91[AFR][1000 genomes]
rs28603269	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:5 , 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	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
4	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
5	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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110293400-110352200	Weak transcription	Gastric	stomach
2	chr2:110297400-110351600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
6	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
7	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
8	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
10	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:110318200-110348400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:110319200-110367400	Weak transcription	HSMMtube	muscle
14	chr2:110319400-110358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:110320600-110354600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:110324000-110348400	Weak transcription	Hela-S3	cervix
17	chr2:110324000-110370400	Weak transcription	Esophagus	oesophagus
18	chr2:110324200-110348600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:110324600-110362200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:110328800-110349000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:110329000-110369000	Weak transcription	Ovary	ovary
22	chr2:110329200-110359400	Weak transcription	NHLF	lung
23	chr2:110329200-110369400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:110329400-110359600	Weak transcription	NHDF-Ad	bronchial
25	chr2:110329600-110351200	Weak transcription	HMEC	breast
26	chr2:110329600-110351600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:110329800-110351600	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:110332200-110352600	Weak transcription	Fetal Lung	lung
29	chr2:110336600-110348600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:110338600-110354600	Weak transcription	Right Atrium	heart
31	chr2:110338600-110357600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:110338800-110352600	Weak transcription	Fetal Intestine Large	intestine
33	chr2:110341000-110351600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:110341600-110349200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:110341600-110359400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:110341800-110348600	Weak transcription	Fetal Heart	heart
37	chr2:110341800-110359000	Weak transcription	Fetal Kidney	kidney
38	chr2:110342800-110351600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:110343400-110348400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:110343400-110348600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:110343400-110348600	Weak transcription	A549	lung
42	chr2:110343400-110350000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:110343400-110352000	Weak transcription	NH-A	brain
44	chr2:110343400-110357600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:110343400-110357600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:110343400-110358000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:110343400-110358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:110343400-110358600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:110343400-110358800	Weak transcription	Adipose Nuclei	Adipose
50	chr2:110343400-110362200	Weak transcription	Psoas Muscle	Psoas

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