Variant report

Variant	rs2319888
Chromosome Location	chr4:69235041-69235042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:69194867..69197488-chr4:69233410..69236002,2	MCF-7	breast:
2	chr4:69210254..69212514-chr4:69233666..69236534,2	MCF-7	breast:
3	chr4:69227116..69229844-chr4:69232808..69235424,3	MCF-7	breast:
4	chr4:69218330..69220312-chr4:69233366..69236029,2	MCF-7	breast:
5	chr4:69208163..69209683-chr4:69233967..69235522,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083896	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11726194	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11727878	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13124352	0.87[ASN][1000 genomes]
rs13130430	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1406694	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17089267	0.84[ASN][1000 genomes]
rs1715080	0.81[ASN][1000 genomes]
rs1715081	0.81[ASN][1000 genomes]
rs1730873	0.84[ASN][1000 genomes]
rs1919898	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2319891	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28656921	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34419508	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34452677	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34500620	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34966613	0.80[AMR][1000 genomes]
rs35632454	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35964416	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36098059	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36126120	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3797008	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4428356	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4860931	0.81[ASN][1000 genomes]
rs6812178	0.84[ASN][1000 genomes]
rs7666993	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2757061	chr4:69178920-69631668	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv437385	chr4:69204755-69383357	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv437386	chr4:69213885-69383357	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1006223	chr4:69217756-69540013	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv870075	chr4:69218674-69608683	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv3407776	chr4:69222857-69376755	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv3442208	chr4:69222907-69288205	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv879223	chr4:69223057-69592846	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	esv3397664	chr4:69223455-69592846	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	esv3468149	chr4:69223455-69592846	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	esv3468150	chr4:69223455-69592846	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69231000-69237200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:69232200-69255600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:69232600-69235800	Enhancers	NH-A	brain
4	chr4:69233000-69235200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
5	chr4:69233600-69235200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
6	chr4:69233800-69235400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr4:69233800-69235400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:69233800-69235400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:69234000-69235200	Weak transcription	HSMMtube	muscle
10	chr4:69234200-69235200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:69234200-69235600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr4:69234200-69239200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:69234200-69242000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:69234400-69235200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:69234400-69235200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:69234600-69235200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:69234600-69235400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:69234600-69235400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr4:69234600-69235400	Enhancers	HepG2	liver
20	chr4:69234600-69235600	Enhancers	Ovary	ovary
21	chr4:69234600-69235600	Enhancers	Hela-S3	cervix
22	chr4:69234600-69239200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr4:69234800-69235200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:69234800-69235200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:69234800-69235400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:69234800-69235400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:69234800-69235400	Flanking Active TSS	HMEC	breast
28	chr4:69234800-69235400	Flanking Active TSS	NHEK	skin
29	chr4:69234800-69235400	Flanking Active TSS	Osteobl	bone
30	chr4:69234800-69235600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:69234800-69236200	Enhancers	Placenta	Placenta
32	chr4:69234800-69238000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:69234800-69239000	Weak transcription	Fetal Kidney	kidney
34	chr4:69234800-69239200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr4:69234800-69239200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr4:69235000-69235400	Flanking Active TSS	A549	lung
37	chr4:69235000-69235600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr4:69235000-69235600	Enhancers	NHDF-Ad	bronchial
39	chr4:69235000-69238400	Weak transcription	HSMM	muscle

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