Variant report

Variant	rs59248614
Chromosome Location	chr2:47567033-47567034
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47566070..47570145-chr2:47570557..47573668,13	MCF-7	breast:
2	chr2:47559485..47574826-chr2:47594341..47605593,65	MCF-7	breast:
3	chr2:47559153..47564945-chr2:47565621..47568941,6	MCF-7	breast:
4	chr2:47560518..47577182-chr2:47592669..47600258,43	MCF-7	breast:
5	chr2:47401975..47404252-chr2:47566491..47569766,3	K562	blood:
6	chr2:47561955..47564861-chr2:47565675..47567222,2	MCF-7	breast:
7	chr2:47564797..47567861-chr2:47601671..47605463,3	MCF-7	breast:
8	chr2:47565883..47568110-chr2:47570627..47573327,3	K562	blood:
9	chr2:47566903..47567946-chr2:47595827..47596958,4	MCF-7	breast:
10	chr2:47565961..47567793-chr2:47603146..47605912,3	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPCAM-1	chr2:47558199-47571656	ENSG00000236824
2	lnc-CALM2-11	chr2:47566664-47568440	ucscGeneNc_uc002rwa_2

No data

Variant related genes	Relation type
ENSG00000234690	Chromatin interaction
ENSG00000207923	Chromatin interaction
ENSG00000119888	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs57945178	1.00[AMR][1000 genomes]
rs58882508	1.00[AMR][1000 genomes]
rs58931241	1.00[AMR][1000 genomes]
rs59927838	1.00[AMR][1000 genomes]
rs60358586	1.00[AMR][1000 genomes]
rs60518577	1.00[AMR][1000 genomes]
rs60887102	1.00[AMR][1000 genomes]
rs60998282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61451736	1.00[AMR][1000 genomes]
rs72882704	1.00[AMR][1000 genomes]
rs72882709	1.00[AMR][1000 genomes]
rs72882712	1.00[AMR][1000 genomes]
rs72882715	1.00[AMR][1000 genomes]
rs72882770	1.00[AMR][1000 genomes]
rs72884694	1.00[AMR][1000 genomes]
rs72884701	1.00[AMR][1000 genomes]
rs72886311	1.00[AMR][1000 genomes]
rs72886331	1.00[AMR][1000 genomes]
rs72886333	1.00[AMR][1000 genomes]
rs72886340	1.00[AMR][1000 genomes]
rs72886346	1.00[AMR][1000 genomes]
rs72886357	1.00[AMR][1000 genomes]
rs72886367	1.00[AMR][1000 genomes]
rs72888235	1.00[AMR][1000 genomes]
rs72888241	1.00[AMR][1000 genomes]
rs72888249	1.00[AMR][1000 genomes]
rs72888257	1.00[AMR][1000 genomes]
rs72888260	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv524003	chr2:47543245-47590034	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv581756	chr2:47552706-47590930	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1009586	chr2:47552706-47621487	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47551200-47572400	Weak transcription	Lung	lung
2	chr2:47552600-47570000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:47560400-47567200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:47560600-47567200	Weak transcription	Fetal Brain Female	brain
5	chr2:47561800-47569400	Weak transcription	Fetal Brain Male	brain
6	chr2:47561800-47571400	Weak transcription	Brain Substantia Nigra	brain
7	chr2:47562000-47567200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:47562200-47567400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:47562200-47570200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:47562400-47567200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:47562400-47570200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:47563600-47570200	Weak transcription	Fetal Kidney	kidney
13	chr2:47563800-47567400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:47563800-47567600	Weak transcription	Small Intestine	intestine
15	chr2:47563800-47570200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:47563800-47570400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:47563800-47571000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:47563800-47571400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:47564000-47567200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:47564000-47569800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:47564000-47570400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:47564000-47570400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:47564000-47570600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:47564200-47567400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:47564200-47567600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:47564200-47570400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:47564200-47570400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:47564400-47567200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:47564400-47567400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:47564400-47567400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:47564400-47567400	Weak transcription	Gastric	stomach
32	chr2:47564400-47567800	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:47564600-47567200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:47564600-47567400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:47564600-47567400	Weak transcription	Fetal Lung	lung
36	chr2:47564600-47567400	Weak transcription	Right Ventricle	heart
37	chr2:47564600-47567600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:47564600-47567600	Weak transcription	Brain Germinal Matrix	brain
39	chr2:47564600-47567800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:47564600-47569600	Weak transcription	Spleen	Spleen
41	chr2:47564600-47571400	Weak transcription	Brain Anterior Caudate	brain
42	chr2:47564800-47567200	Weak transcription	Fetal Stomach	stomach
43	chr2:47564800-47567200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:47564800-47567400	Weak transcription	Colonic Mucosa	Colon
45	chr2:47564800-47571200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:47565000-47567400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:47565000-47572000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:47566400-47567400	Enhancers	Duodenum Mucosa	Duodenum
49	chr2:47566400-47568000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:47566400-47569800	Genic enhancers	Fetal Intestine Small	intestine

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