Variant report

Variant	rs16969789
Chromosome Location	chr15:40040397-40040398
allele	A/G
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	CEBPB	chr15:40040393-40040981	A549	lung:	n/a	n/a
2	EP300	chr15:40040383-40040882	A549	lung:	n/a	n/a
3	TCF12	chr15:40040222-40040983	A549	lung:	n/a	n/a
4	EP300	chr15:40040369-40040868	A549	lung:	n/a	n/a
5	FOXA1	chr15:40040352-40040851	A549	lung:	n/a	n/a
6	SP1	chr15:40040365-40040946	A549	lung:	n/a	n/a
7	STAT3	chr15:40040343-40040846	MCF10A-Er-Src	breast:	n/a	n/a
8	SP1	chr15:40040385-40040969	A549	lung:	n/a	n/a

Variant related genes	Relation type
FSIP1	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1021410	0.93[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1027232	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10520144	1.00[CEU][hapmap]
rs11858148	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12437837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12440567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12442952	1.00[CEU][hapmap]
rs1491624	0.81[JPT][hapmap]
rs1565559	0.81[JPT][hapmap]
rs1565561	0.80[JPT][hapmap]
rs16952186	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs16969621	0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16969802	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1844863	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1906166	1.00[ASN][1000 genomes]
rs2029584	0.80[JPT][hapmap]
rs2171312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28538495	0.94[ASN][1000 genomes]
rs28668904	0.82[AFR][1000 genomes]
rs28884199	0.94[ASN][1000 genomes]
rs28896916	0.94[ASN][1000 genomes]
rs34320375	0.81[ASN][1000 genomes]
rs4923838	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4924379	0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924383	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4924387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4924388	0.94[ASN][1000 genomes]
rs4924390	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs4924392	0.89[ASN][1000 genomes]
rs59180773	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59434895	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60431166	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61620785	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61695850	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62004808	0.81[ASN][1000 genomes]
rs7173020	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7179742	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs7179838	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7180846	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs8024166	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8032864	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8034520	0.85[JPT][hapmap]
rs8034550	0.86[JPT][hapmap]
rs8035291	1.00[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8035986	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs951374	0.89[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	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
2	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
3	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40035000-40040400	Weak transcription	Adipose Nuclei	Adipose
2	chr15:40035600-40050000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:40037800-40041400	Enhancers	Hela-S3	cervix
4	chr15:40038000-40040400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:40038400-40040800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:40038400-40041200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:40038400-40041200	Enhancers	Osteobl	bone
8	chr15:40038600-40041200	Enhancers	NHDF-Ad	bronchial
9	chr15:40039200-40041000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr15:40039400-40040800	Enhancers	NHEK	skin
11	chr15:40039400-40049000	Weak transcription	HUVEC	blood vessel
12	chr15:40039600-40040400	Enhancers	HSMM	muscle
13	chr15:40039600-40040800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:40039800-40041000	Enhancers	Rectal Smooth Muscle	rectum
15	chr15:40040000-40040800	Enhancers	HMEC	breast
16	chr15:40040200-40040400	Flanking Active TSS	A549	lung
17	chr15:40040200-40040800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr15:40040200-40040800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:40040200-40040800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr15:40040200-40041000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:40040200-40041000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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