Variant report

Variant	rs28690295
Chromosome Location	chr4:53801247-53801248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53794290..53797029-chr4:53800788..53802475,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10004829	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014061	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014144	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030623	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10034233	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049923	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331609	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167293	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698672	0.83[ASN][1000 genomes]
rs2086727	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2200225	0.83[ASN][1000 genomes]
rs28432778	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454037	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28472535	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28491101	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28508082	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564509	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28610009	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615713	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28678012	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28786135	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930104	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930105	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930106	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301096	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301098	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301099	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301103	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301104	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301113	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301114	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301116	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443054	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458513	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833350	0.83[ASN][1000 genomes]
rs6855240	0.83[ASN][1000 genomes]
rs7658319	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677726	0.83[ASN][1000 genomes]
rs7680614	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996166	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9998405	0.94[EUR][1000 genomes];1.00[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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
2	chr4:53734600-53822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:53768800-53815600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:53769000-53804400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr4:53786600-53861400	Weak transcription	Primary B cells from cord blood	blood
6	chr4:53793000-53805600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:53796400-53809800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:53797200-53804000	Weak transcription	GM12878-XiMat	blood
9	chr4:53797600-53808400	Weak transcription	Ovary	ovary
10	chr4:53797800-53801400	Weak transcription	Stomach Mucosa	stomach
11	chr4:53798200-53803800	Weak transcription	Gastric	stomach
12	chr4:53798200-53812200	Weak transcription	Fetal Brain Female	brain
13	chr4:53799400-53806000	Weak transcription	HSMMtube	muscle
14	chr4:53799600-53806000	Weak transcription	Left Ventricle	heart
15	chr4:53799600-53809800	Weak transcription	HSMM	muscle
16	chr4:53799600-53820200	Weak transcription	Fetal Stomach	stomach
17	chr4:53799800-53805600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:53800000-53801400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:53800000-53801800	Enhancers	Pancreas	Pancrea
20	chr4:53800200-53806000	Weak transcription	Psoas Muscle	Psoas
21	chr4:53800200-53815600	Weak transcription	Primary T cells from cord blood	blood
22	chr4:53800200-53816600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:53800400-53801400	Enhancers	Placenta	Placenta
24	chr4:53800400-53823000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:53800800-53805000	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:53800800-53805600	Weak transcription	NHDF-Ad	bronchial
27	chr4:53800800-53809800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:53801000-53801400	Enhancers	Fetal Intestine Large	intestine
29	chr4:53801000-53802000	Enhancers	Liver	Liver
30	chr4:53801000-53802000	Enhancers	Hela-S3	cervix

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