Variant report

Variant	rs72731469
Chromosome Location	chr15:40542705-40542706
allele	C/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	TCF12	chr15:40541486-40542768	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr15:40541490-40542744	SK-N-SH	brain:	n/a	chr15:40541900-40541908
3	GATA3	chr15:40541441-40542785	SK-N-SH	brain:	n/a	chr15:40541900-40541908

No.	Distal block	Cell Line	Cell type
1	chr15:40530073..40532673-chr15:40541627..40543957,2	K562	blood:
2	chr15:40529555..40532139-chr15:40538682..40542802,5	MCF-7	breast:
3	chr15:40541959..40544073-chr15:40547668..40550577,3	MCF-7	breast:

Variant related genes	Relation type
PAK6	TF binding region
ENSG00000137843	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1048163	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048164	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11634057	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634409	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636097	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638662	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638733	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050520	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55799438	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55863440	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55974545	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731470	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900054	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	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
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40533800-40543400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:40534000-40544400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr15:40538200-40544200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:40538400-40543400	Weak transcription	Pancreas	Pancrea
5	chr15:40539600-40543200	Weak transcription	Fetal Intestine Large	intestine
6	chr15:40539800-40543200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:40540600-40542800	Enhancers	HMEC	breast
8	chr15:40540600-40543200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:40540800-40542800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:40541000-40543200	Weak transcription	Fetal Heart	heart
11	chr15:40541400-40542800	Enhancers	Hela-S3	cervix
12	chr15:40541800-40542800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:40541800-40542800	Enhancers	HSMM	muscle
14	chr15:40541800-40542800	Enhancers	HUVEC	blood vessel
15	chr15:40541800-40543200	Enhancers	Esophagus	oesophagus
16	chr15:40542000-40543800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:40542200-40543400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr15:40542200-40544600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr15:40542400-40542800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:40542400-40543200	Enhancers	NHEK	skin
21	chr15:40542400-40543400	Weak transcription	Left Ventricle	heart
22	chr15:40542400-40543400	Weak transcription	Right Ventricle	heart
23	chr15:40542400-40543800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:40542400-40543800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:40542400-40544200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:40542400-40544600	Weak transcription	Brain Anterior Caudate	brain
27	chr15:40542400-40544800	Weak transcription	Brain Angular Gyrus	brain
28	chr15:40542600-40543200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:40542600-40543800	Enhancers	Fetal Intestine Small	intestine
30	chr15:40542600-40544200	Weak transcription	Lung	lung
31	chr15:40542600-40544200	Weak transcription	Right Atrium	heart
32	chr15:40542600-40544200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:40542600-40544800	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links