Variant report

Variant	rs60518577
Chromosome Location	chr2:47559920-47559921
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47559485..47574826-chr2:47594341..47605593,65	MCF-7	breast:
2	chr2:47559153..47564945-chr2:47565621..47568941,6	MCF-7	breast:
3	chr2:47402699..47404738-chr2:47559190..47561932,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPCAM-1	chr2:47558199-47571656	ENSG00000236824
2	lnc-CALM2-2	chr2:47549983-47560165	NONHSAT070563

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

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs57945178	1.00[AMR][1000 genomes]
rs58882508	1.00[AMR][1000 genomes]
rs58931241	1.00[AMR][1000 genomes]
rs59248614	1.00[AMR][1000 genomes]
rs59927838	1.00[AMR][1000 genomes]
rs60887102	1.00[AMR][1000 genomes]
rs60998282	1.00[AMR][1000 genomes]
rs61451736	1.00[AMR][1000 genomes]
rs72882704	1.00[AMR][1000 genomes]
rs72882709	1.00[AMR][1000 genomes]
rs72882712	0.83[AFR][1000 genomes];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]

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:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47543200-47563400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:47549000-47563400	Weak transcription	Spleen	Spleen
3	chr2:47549200-47561200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:47549200-47563600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:47550400-47563200	Weak transcription	Fetal Kidney	kidney
6	chr2:47550400-47563800	Weak transcription	Gastric	stomach
7	chr2:47550400-47565200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:47550600-47563400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:47550800-47561400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:47550800-47561400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:47550800-47563400	Weak transcription	Brain Angular Gyrus	brain
12	chr2:47550800-47563400	Weak transcription	Right Atrium	heart
13	chr2:47551000-47560600	Strong transcription	Fetal Intestine Small	intestine
14	chr2:47551000-47561400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:47551000-47561400	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:47551000-47561400	Weak transcription	Brain Substantia Nigra	brain
17	chr2:47551000-47563400	Weak transcription	Colonic Mucosa	Colon
18	chr2:47551000-47563400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:47551000-47563400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:47551000-47564000	Weak transcription	Stomach Mucosa	stomach
21	chr2:47551000-47565600	Weak transcription	Ovary	ovary
22	chr2:47551200-47561400	Weak transcription	A549	lung
23	chr2:47551200-47572400	Weak transcription	Lung	lung
24	chr2:47552600-47570000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:47552800-47560600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:47555800-47560600	Strong transcription	Fetal Stomach	stomach
27	chr2:47556000-47560800	Strong transcription	HepG2	liver
28	chr2:47557400-47561400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:47557600-47560600	Strong transcription	Brain Germinal Matrix	brain
30	chr2:47557800-47560200	Weak transcription	K562	blood
31	chr2:47557800-47560400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr2:47557800-47560400	Strong transcription	Fetal Lung	lung
33	chr2:47558000-47560200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:47558200-47560600	Strong transcription	Fetal Brain Female	brain
35	chr2:47558600-47560000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:47558600-47560600	Strong transcription	Fetal Intestine Large	intestine
37	chr2:47559000-47560000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:47559000-47562400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr2:47559200-47560400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:47559200-47560600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:47559400-47560000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr2:47559400-47560000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:47559400-47560000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:47559400-47560400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:47559400-47560600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr2:47559400-47560800	Enhancers	H1 Cell Line	embryonic stem cell
47	chr2:47559400-47560800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:47559400-47561400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:47559400-47561400	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr2:47559400-47562400	Enhancers	HUES48 Cell Line	embryonic stem cell

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