Variant report

Variant	rs936690
Chromosome Location	chr4:53691035-53691036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53582665..53585471-chr4:53689497..53692252,2	K562	blood:
2	chr4:53577830..53580008-chr4:53690583..53692647,2	MCF-7	breast:
3	chr4:53577643..53580213-chr4:53690826..53692756,2	K562	blood:
4	chr4:53689461..53691750-chr4:53727017..53729673,2	MCF-7	breast:
5	chr4:53689894..53692436-chr4:53702334..53704274,2	MCF-7	breast:
6	chr4:53690322..53693293-chr4:53696846..53698754,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128045	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000226950	Chromatin interaction
ENSG00000264585	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10003908	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016904	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10023440	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10026162	0.86[ASN][1000 genomes]
rs10032097	0.86[EUR][1000 genomes]
rs10032190	0.81[AMR][1000 genomes]
rs1047959	0.85[MEX][hapmap]
rs11940896	0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs11941841	0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.84[AMR][1000 genomes]
rs11947787	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2017237	0.85[MEX][hapmap]
rs4864676	0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4864678	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4864680	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4864685	0.83[AMR][1000 genomes]
rs62336790	0.86[AMR][1000 genomes]
rs62338810	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554056	0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs6844680	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes]
rs730246	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730247	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731073	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7663943	0.85[CHB][hapmap];0.84[AMR][1000 genomes]
rs7692692	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8287	0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.81[AMR][1000 genomes]
rs881743	0.83[JPT][hapmap];0.84[AMR][1000 genomes]
rs962416	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9995861	0.85[AMR][1000 genomes];0.87[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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53688600-53692400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:53688600-53692400	Enhancers	NHDF-Ad	bronchial
3	chr4:53688600-53692600	Enhancers	HMEC	breast
4	chr4:53688800-53692200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:53688800-53692400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:53688800-53692400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:53688800-53692600	Enhancers	Ovary	ovary
8	chr4:53689000-53692000	Enhancers	Fetal Lung	lung
9	chr4:53689000-53692600	Enhancers	Placenta	Placenta
10	chr4:53689000-53693000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:53689200-53692200	Enhancers	NH-A	brain
12	chr4:53689200-53692200	Enhancers	NHLF	lung
13	chr4:53689200-53692600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr4:53689400-53691800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:53689400-53692200	Enhancers	Fetal Stomach	stomach
16	chr4:53689400-53693000	Enhancers	Fetal Heart	heart
17	chr4:53689600-53692200	Enhancers	Right Ventricle	heart
18	chr4:53690000-53692400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:53690000-53692400	Enhancers	Gastric	stomach
20	chr4:53690000-53693000	Enhancers	Fetal Muscle Leg	muscle
21	chr4:53690200-53691200	Weak transcription	Lung	lung
22	chr4:53690200-53691200	Weak transcription	HSMM	muscle
23	chr4:53690200-53691600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:53690400-53691400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:53690400-53691400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:53690400-53691600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:53690400-53691600	Enhancers	Stomach Mucosa	stomach
28	chr4:53690400-53691800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:53690400-53691800	Enhancers	Right Atrium	heart
30	chr4:53690400-53692400	Enhancers	Fetal Muscle Trunk	muscle
31	chr4:53690400-53692400	Enhancers	Psoas Muscle	Psoas
32	chr4:53690600-53691400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:53690600-53691600	Enhancers	Duodenum Mucosa	Duodenum
34	chr4:53690600-53691600	Weak transcription	NHEK	skin
35	chr4:53690600-53691800	Enhancers	Left Ventricle	heart
36	chr4:53690600-53692000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:53690600-53692400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:53690600-53692600	Enhancers	Pancreas	Pancrea
39	chr4:53690600-53693000	Enhancers	Fetal Kidney	kidney
40	chr4:53690800-53691200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:53690800-53691600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr4:53690800-53691800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:53690800-53691800	Enhancers	Colon Smooth Muscle	Colon
44	chr4:53690800-53691800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr4:53690800-53692000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr4:53690800-53692000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr4:53690800-53692200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:53691000-53691200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr4:53691000-53691400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:53691000-53691400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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