Variant report

Variant	rs1513821
Chromosome Location	chr4:89975882-89975883
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10009665	0.88[ASN][1000 genomes]
rs11097214	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097215	0.87[ASN][1000 genomes]
rs12509747	0.87[ASN][1000 genomes]
rs12641645	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12643834	0.87[ASN][1000 genomes]
rs12644568	0.87[ASN][1000 genomes]
rs12646713	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12646734	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13124770	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13148714	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1355835	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355838	0.88[ASN][1000 genomes]
rs1708674	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795731	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795732	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037036	0.85[ASN][1000 genomes]
rs2037037	0.85[ASN][1000 genomes]
rs2458546	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2458547	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2464516	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2464517	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670625	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2704597	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869987	0.87[ASN][1000 genomes]
rs2869988	0.87[ASN][1000 genomes]
rs2869990	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4634189	0.87[ASN][1000 genomes]
rs4693221	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4693983	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532099	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6532109	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6532112	0.87[ASN][1000 genomes]
rs6833401	0.92[ASN][1000 genomes]
rs6833424	0.90[ASN][1000 genomes]
rs6833576	0.92[ASN][1000 genomes]
rs6835031	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6854285	0.87[ASN][1000 genomes]
rs72665891	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7440590	0.87[ASN][1000 genomes]
rs756175	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs756176	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7691983	0.87[ASN][1000 genomes]
rs7696844	0.87[ASN][1000 genomes]
rs938264	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs938268	0.87[ASN][1000 genomes]
rs9991151	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
2	chr4:89973200-89977000	Weak transcription	Psoas Muscle	Psoas
3	chr4:89973400-89976400	Weak transcription	Fetal Intestine Small	intestine
4	chr4:89973400-89976800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:89973400-89977800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:89973400-89977800	Weak transcription	Right Ventricle	heart
7	chr4:89973600-89977800	Weak transcription	Placenta	Placenta
8	chr4:89974000-89976000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:89974400-89976000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:89974400-89976200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:89974600-89976400	Enhancers	Fetal Lung	lung
12	chr4:89974600-89976600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:89975000-89976000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:89975000-89976000	Active TSS	GM12878-XiMat	blood
15	chr4:89975000-89976200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:89975000-89976200	Weak transcription	NHDF-Ad	bronchial
17	chr4:89975200-89976000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:89975200-89976200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr4:89975200-89976200	Enhancers	A549	lung
20	chr4:89975200-89976400	Enhancers	Colon Smooth Muscle	Colon
21	chr4:89975200-89976800	Enhancers	Fetal Heart	heart
22	chr4:89975200-89977200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:89975200-89979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:89975400-89976000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:89975400-89976200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr4:89975400-89976200	Enhancers	HMEC	breast
27	chr4:89975400-89976200	Flanking Active TSS	K562	blood
28	chr4:89975400-89976600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr4:89975400-89976600	Enhancers	HUVEC	blood vessel
30	chr4:89975400-89977000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr4:89975400-89977000	Enhancers	Primary hematopoietic stem cells	blood
32	chr4:89975600-89976000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr4:89975600-89976000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr4:89975600-89976000	Weak transcription	Aorta	Aorta
35	chr4:89975600-89976200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:89975600-89976200	Enhancers	Fetal Muscle Leg	muscle
37	chr4:89975600-89976600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr4:89975600-89976600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr4:89975600-89976600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:89975600-89976800	Enhancers	Fetal Intestine Large	intestine
41	chr4:89975600-89977000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr4:89975600-89977000	Weak transcription	Fetal Brain Male	brain
43	chr4:89975600-89977000	Weak transcription	Hela-S3	cervix
44	chr4:89975600-89977800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:89975600-89978400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:89975600-89978800	Active TSS	Duodenum Mucosa	Duodenum
47	chr4:89975800-89976000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:89975800-89976000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:89975800-89976000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:89975800-89976000	Enhancers	Fetal Stomach	stomach

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