Variant report

Variant	rs12987877
Chromosome Location	chr2:20384706-20384707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20380951..20386083-chr2:20391129..20397009,8	MCF-7	breast:
2	chr2:20377278..20381105-chr2:20382551..20387503,5	K562	blood:
3	chr2:20337465..20342202-chr2:20382545..20388364,6	MCF-7	breast:
4	chr2:20342469..20346864-chr2:20382569..20386022,5	MCF-7	breast:
5	chr2:20383626..20385611-chr2:20385923..20390219,5	MCF-7	breast:
6	chr2:20312519..20315301-chr2:20382441..20384884,2	MCF-7	breast:
7	chr2:20250231..20252461-chr2:20383464..20385595,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223734	Chromatin interaction
ENSG00000068697	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12991571	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4392207	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4666371	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4666373	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71435550	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv997958	chr2:20349343-20386339	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1005524	chr2:20349343-20388138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv998067	chr2:20350751-20386339	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1001531	chr2:20350751-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1007926	chr2:20350751-20393557	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20376200-20386200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:20377200-20386200	Enhancers	Esophagus	oesophagus
3	chr2:20377200-20388200	Enhancers	Stomach Mucosa	stomach
4	chr2:20377400-20384800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:20377400-20390000	Enhancers	Placenta	Placenta
6	chr2:20377600-20386000	Enhancers	Liver	Liver
7	chr2:20378400-20386600	Enhancers	HMEC	breast
8	chr2:20380000-20385200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:20380400-20385000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:20380400-20385800	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr2:20381400-20386400	Enhancers	NHEK	skin
12	chr2:20381400-20387200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:20381600-20386200	Enhancers	Hela-S3	cervix
14	chr2:20381600-20387400	Enhancers	NH-A	brain
15	chr2:20381600-20388000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:20382200-20386600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:20382200-20386800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:20382600-20385200	Enhancers	Gastric	stomach
19	chr2:20383000-20385400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:20383000-20385800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:20383000-20385800	Weak transcription	K562	blood
22	chr2:20383400-20386000	Enhancers	Fetal Intestine Large	intestine
23	chr2:20383600-20384800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:20383600-20384800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:20383600-20385600	Enhancers	Fetal Intestine Small	intestine
26	chr2:20383600-20386400	Enhancers	Pancreas	Pancrea
27	chr2:20383600-20386600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:20383600-20386800	Enhancers	HSMM	muscle
29	chr2:20383800-20389400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:20384000-20386000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:20384000-20386000	Enhancers	Colonic Mucosa	Colon
32	chr2:20384200-20385800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:20384200-20385800	Enhancers	Fetal Lung	lung
34	chr2:20384200-20386200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr2:20384200-20386800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr2:20384200-20388800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:20384200-20389400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr2:20384200-20389600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr2:20384400-20385200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr2:20384400-20386000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:20384400-20386400	Enhancers	Lung	lung
42	chr2:20384400-20387000	Enhancers	Primary hematopoietic stem cells	blood
43	chr2:20384400-20387000	Enhancers	Fetal Muscle Leg	muscle
44	chr2:20384400-20389800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:20384600-20384800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:20384600-20384800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:20384600-20385000	Weak transcription	Fetal Kidney	kidney
48	chr2:20384600-20385000	Enhancers	HepG2	liver
49	chr2:20384600-20385600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:20384600-20385600	Weak transcription	Rectal Mucosa Donor 29	rectum

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