Variant report

Variant	rs990085
Chromosome Location	chr4:90754771-90754772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10005233	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10008964	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10028246	0.85[ASN][1000 genomes]
rs1348224	0.87[ASN][1000 genomes]
rs1372517	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1372518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372520	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372521	0.85[ASN][1000 genomes]
rs1372522	0.82[ASN][1000 genomes]
rs1442144	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1442148	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1471483	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1471484	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1811442	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1811443	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1822217	0.85[ASN][1000 genomes]
rs1837891	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs184810	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2197120	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2245801	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2301134	0.90[ASN][1000 genomes]
rs2301135	0.91[ASN][1000 genomes]
rs2572318	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2572320	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2583962	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2583964	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2583968	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2583972	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2583975	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2583978	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619341	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619347	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2619349	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2619355	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2619356	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619368	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2736994	0.82[AMR][1000 genomes]
rs2737002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2737010	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2737011	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2737021	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2737025	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2737028	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2737030	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28415623	0.83[ASN][1000 genomes]
rs28507349	0.85[ASN][1000 genomes]
rs3113355	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs356162	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356186	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs356188	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356191	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356196	0.81[AFR][1000 genomes]
rs356197	0.81[AFR][1000 genomes]
rs356198	0.81[AFR][1000 genomes]
rs3756059	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3756063	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3806789	0.84[ASN][1000 genomes]
rs4293762	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58864428	0.85[ASN][1000 genomes]
rs6532191	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6532192	0.87[ASN][1000 genomes]
rs6532193	0.87[ASN][1000 genomes]
rs6816736	0.85[ASN][1000 genomes]
rs6817001	0.85[ASN][1000 genomes]
rs6828271	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6843084	0.85[ASN][1000 genomes]
rs748849	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7680557	0.87[ASN][1000 genomes]
rs7680761	0.87[ASN][1000 genomes]
rs7681154	0.84[ASN][1000 genomes]
rs7681440	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7687945	0.87[ASN][1000 genomes]
rs894280	0.87[ASN][1000 genomes]
rs920624	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90730200-90757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:90730800-90757000	Weak transcription	Fetal Stomach	stomach
3	chr4:90735800-90755600	Weak transcription	Fetal Brain Male	brain
4	chr4:90738000-90755800	Weak transcription	Fetal Brain Female	brain
5	chr4:90738400-90756600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:90743400-90756600	Weak transcription	NHEK	skin
7	chr4:90743400-90757400	Weak transcription	Gastric	stomach
8	chr4:90743800-90756600	Weak transcription	Ovary	ovary
9	chr4:90748800-90755600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:90751000-90756600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:90751000-90756600	Weak transcription	Fetal Thymus	thymus
12	chr4:90751000-90757200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:90751200-90755400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:90751200-90756400	Weak transcription	Primary T cells from cord blood	blood
15	chr4:90751200-90756600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:90751400-90755600	Weak transcription	Brain Angular Gyrus	brain
17	chr4:90751400-90756600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:90751400-90756600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:90751400-90757400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:90751600-90755400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:90751600-90755800	Weak transcription	Brain Anterior Caudate	brain
22	chr4:90751600-90755800	Weak transcription	Brain Substantia Nigra	brain
23	chr4:90751600-90756600	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:90751600-90756800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr4:90751800-90755600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:90751800-90756000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:90752000-90755400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:90752000-90757000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr4:90752200-90755400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:90752200-90755600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:90752200-90756000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:90752600-90756600	Weak transcription	Fetal Lung	lung
33	chr4:90753200-90756000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:90753400-90756600	Genic enhancers	Dnd41	blood
35	chr4:90753600-90755400	Strong transcription	HUVEC	blood vessel
36	chr4:90753600-90756600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:90753800-90754800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:90753800-90757200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:90754600-90756000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:90754600-90756400	Weak transcription	HMEC	breast

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