Variant report

Variant	rs28642817
Chromosome Location	chr2:20779872-20779873
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20777398..20780363-chr2:20792130..20794608,2	MCF-7	breast:
2	chr2:20673517..20675225-chr2:20778394..20780354,2	MCF-7	breast:
3	chr2:20777247..20781087-chr2:20782458..20786081,5	K562	blood:
4	chr2:20664924..20667934-chr2:20777556..20780555,3	MCF-7	breast:
5	chr2:20100218..20102448-chr2:20777945..20780505,2	K562	blood:
6	chr2:20777789..20780759-chr2:20800338..20803588,3	K562	blood:
7	chr2:20644778..20652349-chr2:20775724..20782509,25	MCF-7	breast:
8	chr2:20778568..20780393-chr2:20788647..20790853,2	K562	blood:
9	chr2:20775386..20780947-chr2:20790998..20795393,7	K562	blood:
10	chr2:20772999..20776929-chr2:20778925..20783592,5	MCF-7	breast:
11	chr2:20777677..20780481-chr2:20791638..20794768,3	MCF-7	breast:
12	chr2:20778242..20781356-chr2:20782083..20785108,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000271991	Chromatin interaction
ENSG00000231948	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10176721	0.85[AMR][1000 genomes]
rs10200826	0.85[AMR][1000 genomes]
rs28488411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28529647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28600892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55751815	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55793738	0.92[AFR][1000 genomes]
rs57360378	0.88[AFR][1000 genomes]
rs57494499	0.85[AMR][1000 genomes]
rs57524662	0.85[AMR][1000 genomes]
rs58590712	0.85[AMR][1000 genomes]
rs58696000	0.85[AMR][1000 genomes]
rs58726406	0.90[AFR][1000 genomes]
rs59300971	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59618840	0.90[AFR][1000 genomes]
rs59771803	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59882809	0.85[AMR][1000 genomes]
rs60283906	0.85[AMR][1000 genomes]
rs60759855	0.92[AFR][1000 genomes]
rs61272752	0.92[AFR][1000 genomes]
rs61478003	0.85[AMR][1000 genomes]
rs62124225	0.93[AFR][1000 genomes]
rs62124226	0.93[AFR][1000 genomes]
rs62124227	0.93[AFR][1000 genomes]
rs62124228	0.93[AFR][1000 genomes]
rs62124229	0.93[AFR][1000 genomes]
rs62124230	0.93[AFR][1000 genomes]
rs62124231	0.93[AFR][1000 genomes]
rs62124232	0.93[AFR][1000 genomes]
rs62124234	0.90[AFR][1000 genomes]
rs73235057	0.85[AMR][1000 genomes]
rs73235060	0.85[AMR][1000 genomes]
rs73235063	0.85[AMR][1000 genomes]
rs73235064	0.85[AMR][1000 genomes]
rs73235072	0.85[AMR][1000 genomes]
rs73235100	0.85[AMR][1000 genomes]
rs73237114	0.85[AMR][1000 genomes]
rs73237135	0.85[AMR][1000 genomes]
rs73919913	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919915	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919918	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919920	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919921	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919922	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919923	0.93[AFR][1000 genomes]
rs73919924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919926	0.86[AFR][1000 genomes]
rs73919928	0.93[AFR][1000 genomes]
rs73919930	0.82[AFR][1000 genomes]
rs7564684	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7574045	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7574289	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7588678	0.89[AFR][1000 genomes]
rs7601273	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20765600-20780800	Enhancers	Adipose Nuclei	Adipose
2	chr2:20765800-20786200	Enhancers	HUVEC	blood vessel
3	chr2:20766800-20780800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr2:20766800-20781000	Enhancers	Left Ventricle	heart
5	chr2:20767000-20781000	Enhancers	Right Atrium	heart
6	chr2:20767800-20782600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:20769400-20780000	Enhancers	Fetal Intestine Large	intestine
8	chr2:20769800-20781000	Enhancers	Fetal Muscle Leg	muscle
9	chr2:20772600-20781000	Enhancers	Placenta	Placenta
10	chr2:20772600-20785800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:20772800-20780800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:20773000-20781000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:20773400-20781200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:20773600-20780000	Enhancers	Spleen	Spleen
15	chr2:20773600-20780200	Enhancers	Fetal Heart	heart
16	chr2:20773600-20781000	Enhancers	Lung	lung
17	chr2:20774600-20781000	Enhancers	Fetal Muscle Trunk	muscle
18	chr2:20775200-20780800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr2:20775200-20781000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:20775400-20780000	Enhancers	Fetal Intestine Small	intestine
21	chr2:20776800-20780000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:20777000-20780000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:20777000-20780000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:20777000-20780000	Enhancers	Duodenum Mucosa	Duodenum
25	chr2:20777000-20780000	Enhancers	Right Ventricle	heart
26	chr2:20777000-20780000	Enhancers	HMEC	breast
27	chr2:20777000-20780000	Enhancers	NHEK	skin
28	chr2:20777000-20780800	Enhancers	NHLF	lung
29	chr2:20777000-20781000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:20777000-20781000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:20777000-20781000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:20777000-20781000	Enhancers	Stomach Mucosa	stomach
33	chr2:20777000-20782000	Enhancers	Brain Cingulate Gyrus	brain
34	chr2:20777200-20780000	Enhancers	Psoas Muscle	Psoas
35	chr2:20777200-20780200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:20777200-20780200	Enhancers	NHDF-Ad	bronchial
37	chr2:20777200-20781000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:20777400-20780000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr2:20777400-20780000	Enhancers	Small Intestine	intestine
40	chr2:20777400-20780000	Enhancers	Osteobl	bone
41	chr2:20777600-20780000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:20777600-20780000	Enhancers	Brain Angular Gyrus	brain
43	chr2:20777600-20780200	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr2:20777600-20780400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:20777600-20781000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:20777800-20780000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:20777800-20780000	Enhancers	Brain Anterior Caudate	brain
48	chr2:20777800-20780000	Enhancers	Ovary	ovary
49	chr2:20777800-20780000	Enhancers	HSMM	muscle
50	chr2:20777800-20780200	Enhancers	Colon Smooth Muscle	Colon

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