Variant report

Variant	rs2227287
Chromosome Location	chr3:53892903-53892904
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
ENSG00000016391	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000222888	Chromatin interaction
ENSG00000056736	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11716354	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12637033	1.00[ASN][1000 genomes]
rs12637539	1.00[AMR][1000 genomes]
rs2232350	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28385745	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28385750	0.97[ASN][1000 genomes]
rs28741401	1.00[ASN][1000 genomes]
rs28741402	1.00[ASN][1000 genomes]
rs3733072	0.86[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

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53881000-53893200	Weak transcription	Ovary	ovary
2	chr3:53881200-53895000	Weak transcription	A549	lung
3	chr3:53881200-53895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:53881400-53893000	Weak transcription	Brain Angular Gyrus	brain
5	chr3:53881400-53893000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:53884000-53895800	Strong transcription	HepG2	liver
7	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
8	chr3:53885400-53895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:53885600-53896600	Weak transcription	Right Ventricle	heart
10	chr3:53886200-53897200	Weak transcription	Colonic Mucosa	Colon
11	chr3:53887800-53898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
13	chr3:53888800-53894400	Weak transcription	Primary T cells from cord blood	blood
14	chr3:53889000-53901400	Weak transcription	Esophagus	oesophagus
15	chr3:53889200-53894400	Strong transcription	Fetal Intestine Small	intestine
16	chr3:53889600-53895200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:53889600-53896000	Strong transcription	Pancreas	Pancrea
18	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:53889800-53893200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:53889800-53895400	Weak transcription	NHDF-Ad	bronchial
21	chr3:53890000-53895800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:53890000-53904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:53890200-53894400	Weak transcription	Aorta	Aorta
24	chr3:53890200-53895800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:53890400-53894400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:53890400-53895200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:53890400-53898600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:53890400-53898800	Weak transcription	NH-A	brain
29	chr3:53890400-53903600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:53890600-53893000	Weak transcription	HSMM	muscle
31	chr3:53890800-53893000	Weak transcription	Placenta	Placenta
32	chr3:53890800-53893200	Weak transcription	HSMMtube	muscle
33	chr3:53890800-53893400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:53891000-53895000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:53891000-53895800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:53891000-53898000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:53891000-53898000	Weak transcription	Spleen	Spleen
39	chr3:53891000-53914200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:53891000-53914200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr3:53891200-53893400	Weak transcription	Primary B cells from cord blood	blood
42	chr3:53891200-53894200	Weak transcription	Osteobl	bone
43	chr3:53891200-53894800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:53891200-53895000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:53891200-53897800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:53891200-53898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:53891200-53900800	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:53891200-53910800	Strong transcription	Fetal Stomach	stomach
49	chr3:53891400-53893200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:53891400-53898400	Weak transcription	Small Intestine	intestine

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