Variant report

Variant	rs13315972
Chromosome Location	chr3:53892553-53892554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53888852..53890407-chr3:53890829..53893730,2	K562	blood:
2	chr3:53878629..53881188-chr3:53889615..53893181,4	MCF-7	breast:
3	chr3:53889294..53893230-chr3:53913823..53917660,4	K562	blood:
4	chr3:53891718..53893662-chr3:53914983..53917466,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113812	Chromatin interaction
ENSG00000056736	Chromatin interaction
ENSG00000016391	Chromatin interaction
ENSG00000222888	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10440151	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1046677	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1134092	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157175	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072145	0.97[ASN][1000 genomes]
rs1982172	0.82[EUR][1000 genomes]
rs1992155	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2083127	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276846	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733073	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733081	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816144	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821867	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569647	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687757	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687763	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7624599	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636856	0.97[ASN][1000 genomes]
rs893367	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9311516	0.97[ASN][1000 genomes]
rs9311518	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9822471	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840362	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9869505	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878207	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878562	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs999514	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13315972	IL17RB	cis	Whole Blood	GTEx
rs13315972	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs13315972	RP11-884K10.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53881000-53892600	Weak transcription	Psoas Muscle	Psoas
2	chr3:53881000-53893200	Weak transcription	Ovary	ovary
3	chr3:53881200-53895000	Weak transcription	A549	lung
4	chr3:53881200-53895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:53881400-53892600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:53881400-53892600	Weak transcription	Hela-S3	cervix
7	chr3:53881400-53892800	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:53881400-53893000	Weak transcription	Brain Angular Gyrus	brain
9	chr3:53881400-53893000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:53884000-53895800	Strong transcription	HepG2	liver
11	chr3:53884400-53892800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
13	chr3:53885400-53892800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:53885400-53895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:53885600-53892600	Weak transcription	Left Ventricle	heart
16	chr3:53885600-53896600	Weak transcription	Right Ventricle	heart
17	chr3:53886200-53897200	Weak transcription	Colonic Mucosa	Colon
18	chr3:53887800-53892800	Weak transcription	Lung	lung
19	chr3:53887800-53898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
21	chr3:53888800-53892600	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:53888800-53894400	Weak transcription	Primary T cells from cord blood	blood
23	chr3:53889000-53901400	Weak transcription	Esophagus	oesophagus
24	chr3:53889200-53892800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:53889200-53894400	Strong transcription	Fetal Intestine Small	intestine
26	chr3:53889400-53892800	Enhancers	GM12878-XiMat	blood
27	chr3:53889600-53892600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:53889600-53892800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:53889600-53892800	Weak transcription	Thymus	Thymus
30	chr3:53889600-53895200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:53889600-53896000	Strong transcription	Pancreas	Pancrea
32	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:53889800-53892800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:53889800-53892800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:53889800-53893200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:53889800-53895400	Weak transcription	NHDF-Ad	bronchial
37	chr3:53890000-53892800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:53890000-53895800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:53890000-53904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:53890200-53892800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:53890200-53894400	Weak transcription	Aorta	Aorta
42	chr3:53890200-53895800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:53890400-53894400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:53890400-53895200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:53890400-53898600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:53890400-53898800	Weak transcription	NH-A	brain
47	chr3:53890400-53903600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:53890600-53893000	Weak transcription	HSMM	muscle
49	chr3:53890800-53893000	Weak transcription	Placenta	Placenta
50	chr3:53890800-53893200	Weak transcription	HSMMtube	muscle

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