Variant report

Variant	rs28648588
Chromosome Location	chr5:68750574-68750575
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr5:68750362-68750659	HepG2	liver:	n/a	n/a
2	MAFK	chr5:68750447-68750920	HepG2	liver:	n/a	chr5:68750505-68750520
3	HEY1	chr5:68750006-68750597	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAF9-4	chr5:68750420-68750892	NONHSAT101919

Variant related genes	Relation type
RN7SL476P	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28366566	0.95[EUR][1000 genomes]
rs28565505	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28635172	0.95[ASN][1000 genomes]
rs28650846	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28652932	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846486	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4274940	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4416560	0.95[EUR][1000 genomes]
rs57859685	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60807929	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73116811	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73116814	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[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	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1023116	chr5:68744307-68867282	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68748800-68751000	Enhancers	Pancreas	Pancrea
2	chr5:68749800-68750600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr5:68750000-68750600	Active TSS	Fetal Intestine Large	intestine
4	chr5:68750000-68750600	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr5:68750000-68751000	Flanking Active TSS	Liver	Liver
6	chr5:68750000-68751000	Active TSS	Duodenum Mucosa	Duodenum
7	chr5:68750000-68751000	Enhancers	Placenta	Placenta
8	chr5:68750200-68750600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:68750200-68750600	Flanking Active TSS	A549	lung
10	chr5:68750200-68750800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:68750200-68750800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:68750200-68750800	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr5:68750200-68750800	Active TSS	Rectal Smooth Muscle	rectum
14	chr5:68750200-68751000	Active TSS	Colonic Mucosa	Colon
15	chr5:68750200-68751200	Flanking Active TSS	HepG2	liver
16	chr5:68750400-68750600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:68750400-68750600	Enhancers	Fetal Intestine Small	intestine
18	chr5:68750400-68750600	Enhancers	Stomach Mucosa	stomach
19	chr5:68750400-68750800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr5:68750400-68750800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr5:68750400-68750800	Enhancers	Primary T cells from cord blood	blood
22	chr5:68750400-68750800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:68750400-68750800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:68750400-68750800	Enhancers	Pancreatic Islets	Pancreatic Islet

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