Variant report

Variant	rs28900716
Chromosome Location	chr2:234759817-234759818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234758197..234760837-chr2:234836027..234838488,2	K562	blood:
2	chr2:234759783..234762312-chr2:234875051..234877633,2	K562	blood:
3	chr2:234753471..234756128-chr2:234758714..234761959,3	MCF-7	breast:
4	chr2:234747927..234752617-chr2:234757241..234760452,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123485	Chromatin interaction
ENSG00000144481	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs28899475	1.00[AMR][1000 genomes]
rs28900418	1.00[AMR][1000 genomes]
rs28900714	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28900976	1.00[AMR][1000 genomes]
rs28946894	1.00[AMR][1000 genomes]
rs35542629	1.00[AMR][1000 genomes]
rs3771333	1.00[AMR][1000 genomes]
rs59046407	1.00[AMR][1000 genomes]
rs61200559	1.00[AMR][1000 genomes]
rs73120730	1.00[AMR][1000 genomes]
rs73120736	1.00[AMR][1000 genomes]
rs73120743	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876023	chr2:234726154-234763137	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234736400-234762600	Weak transcription	Right Atrium	heart
2	chr2:234738200-234762000	Weak transcription	Esophagus	oesophagus
3	chr2:234740000-234760000	Strong transcription	Thymus	Thymus
4	chr2:234740200-234761000	Weak transcription	Primary B cells from cord blood	blood
5	chr2:234740400-234762200	Weak transcription	Primary T cells from cord blood	blood
6	chr2:234741800-234762000	Weak transcription	Gastric	stomach
7	chr2:234742200-234760400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:234742200-234762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:234742600-234760400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:234742600-234760600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:234742600-234760600	Strong transcription	NHEK	skin
12	chr2:234742600-234760800	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr2:234742800-234760400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:234742800-234760600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:234742800-234760600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:234742800-234760800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:234743000-234760000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:234743000-234760000	Strong transcription	HMEC	breast
19	chr2:234743000-234760800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr2:234743000-234760800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:234743000-234761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:234743200-234760200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:234743200-234760600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:234743200-234760600	Strong transcription	Fetal Muscle Leg	muscle
25	chr2:234744000-234760400	Strong transcription	K562	blood
26	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
27	chr2:234744600-234762000	Weak transcription	Colonic Mucosa	Colon
28	chr2:234747800-234760400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:234748000-234760400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:234748000-234760400	Strong transcription	Fetal Stomach	stomach
31	chr2:234748200-234760600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:234748400-234760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:234748600-234762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:234749200-234760400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:234749200-234760400	Strong transcription	Hela-S3	cervix
36	chr2:234749200-234761600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:234749400-234760600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:234750600-234761400	Weak transcription	Fetal Brain Female	brain
39	chr2:234751200-234760800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:234752800-234761600	Weak transcription	Fetal Kidney	kidney
41	chr2:234753200-234760600	Weak transcription	Spleen	Spleen
42	chr2:234753200-234761600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:234753200-234762200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:234753600-234760600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:234753800-234760400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:234755000-234760600	Weak transcription	NH-A	brain
47	chr2:234755200-234761000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:234755200-234761000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:234755200-234761000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:234756200-234760000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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