Variant report

Variant	rs1048163
Chromosome Location	chr15:40543223-40543224
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	CTCF	chr15:40543150-40543331	K562	blood:	n/a	n/a
2	CTCF	chr15:40543165-40543282	K562	blood:	n/a	n/a
3	CTCF	chr15:40543058-40543383	K562	blood:	n/a	n/a
4	CTCF	chr15:40543160-40543310	WERI-Rb-1	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40530073..40532673-chr15:40541627..40543957,2	K562	blood:
2	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: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1048164	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11634057	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634409	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636097	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636147	1.00[JPT][hapmap]
rs11638662	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638733	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050520	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17733008	1.00[JPT][hapmap]
rs2018127	1.00[JPT][hapmap]
rs2289327	1.00[JPT][hapmap]
rs55799438	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55863440	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55974545	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731469	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731470	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040419	1.00[JPT][hapmap]
rs900054	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1048163	RPAP1	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr15:40542000-40543800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:40542200-40543400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr15:40542200-40544600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr15:40542400-40543400	Weak transcription	Left Ventricle	heart
9	chr15:40542400-40543400	Weak transcription	Right Ventricle	heart
10	chr15:40542400-40543800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:40542400-40543800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:40542400-40544200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40542400-40544600	Weak transcription	Brain Anterior Caudate	brain
14	chr15:40542400-40544800	Weak transcription	Brain Angular Gyrus	brain
15	chr15:40542600-40543800	Enhancers	Fetal Intestine Small	intestine
16	chr15:40542600-40544200	Weak transcription	Lung	lung
17	chr15:40542600-40544200	Weak transcription	Right Atrium	heart
18	chr15:40542600-40544200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:40542600-40544800	Weak transcription	Gastric	stomach
20	chr15:40542800-40544000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:40542800-40545200	Weak transcription	HMEC	breast
22	chr15:40543000-40543600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:40543000-40544000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:40543200-40544000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:40543200-40544000	Weak transcription	Esophagus	oesophagus
26	chr15:40543200-40544200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:40543200-40544200	Enhancers	Fetal Heart	heart
28	chr15:40543200-40544200	Enhancers	Fetal Intestine Large	intestine
29	chr15:40543200-40544400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:40543200-40546200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links