Variant report

Variant	rs16969621
Chromosome Location	chr15:39991443-39991444
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39980861..39985158-chr15:39988045..39992700,5	K562	blood:
2	chr15:39989762..39992879-chr15:39994931..39996889,3	K562	blood:
3	chr15:39991324..39992858-chr15:39992903..39994537,2	K562	blood:
4	chr15:39991017..39993549-chr15:40010029..40012182,2	K562	blood:
5	chr15:39984161..39987304-chr15:39989320..39992486,3	K562	blood:
6	chr15:39990318..39992380-chr15:40073130..40075766,2	K562	blood:
7	chr15:39977207..39979159-chr15:39990602..39992278,2	K562	blood:

Variant related genes	Relation type
ENSG00000261136	Chromatin interaction
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10520144	0.90[EUR][1000 genomes]
rs11858148	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs12437837	0.85[JPT][hapmap]
rs12440567	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs12442952	0.80[EUR][1000 genomes]
rs16952186	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16969789	0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16969802	0.85[JPT][hapmap]
rs1906166	0.82[ASN][1000 genomes]
rs2171312	0.85[JPT][hapmap]
rs4923838	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs4924379	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924380	1.00[CHB][hapmap]
rs4924383	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4924387	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs59180773	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59434895	0.94[AMR][1000 genomes]
rs60431166	0.94[AMR][1000 genomes]
rs61620785	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61695850	0.94[AMR][1000 genomes]
rs7173020	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7183539	0.90[EUR][1000 genomes]
rs72727050	0.89[ASN][1000 genomes]
rs8024166	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8032864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034520	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8034550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8035291	0.92[CHB][hapmap];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8035986	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs951374	0.94[AMR][1000 genomes];0.96[ASN][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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39985600-39996600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:39985800-39992000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:39985800-39992200	Weak transcription	Fetal Lung	lung
4	chr15:39985800-39996400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:39985800-39996600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:39988000-39996600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:39989400-39991600	Weak transcription	NHDF-Ad	bronchial
8	chr15:39990600-39991800	Flanking Active TSS	K562	blood
9	chr15:39990600-39992800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:39990600-39993200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:39990800-39992200	Enhancers	Fetal Intestine Large	intestine
12	chr15:39990800-39992400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:39990800-39992400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:39990800-39992400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:39991000-39992400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:39991200-39996600	Weak transcription	Placenta	Placenta

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