Variant report

Variant	rs28517777
Chromosome Location	chr11:86530605-86530606
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	MAFK	chr11:86530516-86530613	HepG2	liver:	n/a	chr11:86530562-86530577 chr11:86530565-86530579

No.	Distal block	Cell Line	Cell type
1	chr11:45823561..45828126-chr11:86528256..86531993,4	MCF-7	breast:
2	chr11:86012430..86015246-chr11:86529732..86532220,2	K562	blood:
3	chr11:86487507..86489179-chr11:86528205..86530836,2	MCF-7	breast:
4	chr11:86525515..86527184-chr11:86529410..86531727,2	K562	blood:
5	chr11:86318542..86319850-chr11:86528941..86530646,11	MCF-7	breast:
6	chr11:86316921..86319182-chr11:86528850..86531026,2	MCF-7	breast:

Variant related genes	Relation type
PRSS23	TF binding region
ENSG00000149196	Chromatin interaction
ENSG00000181830	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12420039	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12421517	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12421942	0.81[ASN][1000 genomes]
rs12574979	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17212012	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17819181	0.98[ASN][1000 genomes]
rs17819187	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1939110	0.83[ASN][1000 genomes]
rs1939111	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1939112	0.95[ASN][1000 genomes]
rs1939113	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1939114	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1939116	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1954769	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2155080	0.94[ASN][1000 genomes]
rs2155081	0.94[ASN][1000 genomes]
rs3809048	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4291699	0.92[ASN][1000 genomes]
rs4304806	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4307748	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4423210	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4485132	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs55646317	0.85[AMR][1000 genomes]
rs58512185	0.88[AMR][1000 genomes]
rs58976693	0.85[AMR][1000 genomes]
rs61707378	0.86[AMR][1000 genomes]
rs7108490	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7118751	0.98[ASN][1000 genomes]
rs7131625	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs744292	0.85[AMR][1000 genomes]
rs7931274	0.97[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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2756074	chr11:86456552-86729552	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv2760199	chr11:86512312-86531118	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86520000-86549200	Weak transcription	Ovary	ovary
2	chr11:86521000-86551400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr11:86522800-86544400	Weak transcription	Fetal Kidney	kidney
4	chr11:86525200-86531000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:86525800-86530800	Enhancers	Rectal Smooth Muscle	rectum
6	chr11:86526800-86531000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:86527400-86531000	Enhancers	Colon Smooth Muscle	Colon
8	chr11:86527800-86534400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:86528000-86542600	Weak transcription	Adipose Nuclei	Adipose
10	chr11:86528800-86545400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:86529000-86530800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:86529000-86530800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:86529600-86543400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr11:86530200-86532000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:86530200-86533400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:86530200-86534200	Weak transcription	NHEK	skin
17	chr11:86530200-86541800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:86530200-86542800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:86530200-86549000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:86530200-86549000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:86530200-86549000	Weak transcription	HMEC	breast
22	chr11:86530200-86550800	Weak transcription	HUVEC	blood vessel
23	chr11:86530400-86531600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:86530400-86531800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr11:86530400-86532600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:86530400-86534000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:86530400-86534200	Weak transcription	HSMM	muscle
28	chr11:86530400-86534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:86530400-86534600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:86530400-86537000	Weak transcription	Fetal Lung	lung
31	chr11:86530400-86548600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:86530400-86549200	Weak transcription	Aorta	Aorta
33	chr11:86530400-86551000	Weak transcription	A549	lung
34	chr11:86530400-86551400	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links