Variant report

Variant	rs28502849
Chromosome Location	chr4:88345448-88345449
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:88344098..88346850-chr4:88347399..88349099,3	MCF-7	breast:
2	chr4:88340563..88342774-chr4:88344260..88346848,4	MCF-7	breast:
3	chr4:88309813..88313902-chr4:88342245..88346379,5	K562	blood:

Variant related genes	Relation type
ENSG00000198189	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10010988	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10025902	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032597	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11945232	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13103927	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13113575	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138404	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13138636	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13150578	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28372775	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406846	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28609242	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28630962	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28701008	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28736552	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34549877	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35322242	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35371368	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4314250	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816224	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6854710	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7659182	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88342600-88346000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:88343000-88345800	Active TSS	HSMM	muscle
3	chr4:88343200-88345800	Active TSS	Fetal Kidney	kidney
4	chr4:88343200-88345800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr4:88343400-88345600	Active TSS	Pancreas	Pancrea
6	chr4:88343400-88346000	Active TSS	H1 Cell Line	embryonic stem cell
7	chr4:88343600-88345600	Active TSS	Hela-S3	cervix
8	chr4:88344400-88346000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:88344400-88346200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:88344400-88346200	Weak transcription	Esophagus	oesophagus
11	chr4:88344400-88346200	Weak transcription	Spleen	Spleen
12	chr4:88344400-88398600	Weak transcription	Gastric	stomach
13	chr4:88344600-88346400	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:88344600-88356200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:88344600-88356200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:88344800-88345600	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr4:88344800-88346400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr4:88345000-88346000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:88345000-88346400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr4:88345000-88346600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:88345200-88345600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:88345200-88345800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr4:88345200-88345800	Enhancers	Brain Cingulate Gyrus	brain
24	chr4:88345200-88345800	Enhancers	Fetal Brain Male	brain
25	chr4:88345200-88345800	Enhancers	Left Ventricle	heart
26	chr4:88345200-88345800	Enhancers	Small Intestine	intestine
27	chr4:88345200-88346000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr4:88345200-88346000	Enhancers	Primary B cells from cord blood	blood
29	chr4:88345200-88346000	Enhancers	Primary T cells from cord blood	blood
30	chr4:88345200-88346000	Weak transcription	Aorta	Aorta
31	chr4:88345200-88346000	Enhancers	Fetal Heart	heart
32	chr4:88345200-88346000	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr4:88345200-88346000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr4:88345200-88346200	Enhancers	Colon Smooth Muscle	Colon
35	chr4:88345200-88346200	Enhancers	Thymus	Thymus
36	chr4:88345200-88346400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr4:88345200-88346400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr4:88345200-88346400	Enhancers	Brain Angular Gyrus	brain
39	chr4:88345200-88346400	Enhancers	Brain Substantia Nigra	brain
40	chr4:88345200-88346400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr4:88345200-88346400	Enhancers	Fetal Brain Female	brain
42	chr4:88345200-88346400	Enhancers	HepG2	liver
43	chr4:88345200-88346600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:88345200-88346800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:88345200-88346800	Enhancers	Lung	lung
46	chr4:88345200-88347200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr4:88345200-88356200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:88345200-88356200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr4:88345200-88356800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:88345200-88362800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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