Variant report

Variant	rs57155672
Chromosome Location	chr2:47569594-47569595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr2:47568329..47569951-chr2:47579574..47581302,2	MCF-7	breast:
4	chr2:47560518..47577182-chr2:47592669..47600258,43	MCF-7	breast:
5	chr2:47401975..47404252-chr2:47566491..47569766,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPCAM-1	chr2:47558199-47571656	ENSG00000236824

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

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs58882508	0.95[AFR][1000 genomes]
rs61451736	0.85[AFR][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:64 , 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	chr2:47561800-47571400	Weak transcription	Brain Substantia Nigra	brain
4	chr2:47562200-47570200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:47562400-47570200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:47563600-47570200	Weak transcription	Fetal Kidney	kidney
7	chr2:47563800-47570200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:47563800-47570400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:47563800-47571000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:47563800-47571400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:47564000-47569800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:47564000-47570400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:47564000-47570400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:47564000-47570600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:47564200-47570400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:47564200-47570400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:47564600-47569600	Weak transcription	Spleen	Spleen
18	chr2:47564600-47571400	Weak transcription	Brain Anterior Caudate	brain
19	chr2:47564800-47571200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:47565000-47572000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:47566400-47569800	Genic enhancers	Fetal Intestine Small	intestine
22	chr2:47567800-47571200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:47567800-47571400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:47567800-47571600	Weak transcription	Gastric	stomach
25	chr2:47568000-47569800	Weak transcription	Fetal Brain Female	brain
26	chr2:47568000-47570200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:47568000-47570200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:47568000-47570800	Weak transcription	NH-A	brain
29	chr2:47568000-47571400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:47568000-47571400	Weak transcription	Right Ventricle	heart
31	chr2:47568000-47571600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:47568000-47572000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:47568000-47572000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:47568000-47572600	Weak transcription	Small Intestine	intestine
35	chr2:47568200-47569600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:47568200-47569600	Enhancers	HepG2	liver
37	chr2:47568200-47569800	Weak transcription	Brain Germinal Matrix	brain
38	chr2:47568200-47569800	Enhancers	Duodenum Mucosa	Duodenum
39	chr2:47568200-47569800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:47568200-47569800	Weak transcription	A549	lung
41	chr2:47568200-47570000	Weak transcription	Pancreas	Pancrea
42	chr2:47568200-47570200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:47568200-47570200	Weak transcription	Fetal Lung	lung
44	chr2:47568200-47570200	Weak transcription	K562	blood
45	chr2:47568200-47570400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:47568200-47570600	Weak transcription	Colonic Mucosa	Colon
47	chr2:47568200-47571000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:47568200-47571400	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:47568200-47571400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:47568200-47571800	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links