Variant report

Variant	rs3857060
Chromosome Location	chr4:90679528-90679529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10516846	0.82[AFR][1000 genomes]
rs10516847	1.00[YRI][hapmap]
rs17016074	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17016083	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17016100	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17016107	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17016124	0.83[AFR][1000 genomes]
rs17016126	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2882785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34094566	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34351491	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34356244	0.83[AFR][1000 genomes]
rs34747217	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35683448	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35771728	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35921673	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3729594	1.00[YRI][hapmap]
rs3775435	1.00[YRI][hapmap]
rs3775438	0.93[YRI][hapmap]
rs3775442	1.00[YRI][hapmap]
rs3775444	1.00[YRI][hapmap]
rs3775450	1.00[YRI][hapmap]
rs3796662	0.83[AFR][1000 genomes]
rs3822088	1.00[YRI][hapmap]
rs3822091	1.00[YRI][hapmap]
rs3857054	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3857056	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3898322	1.00[YRI][hapmap]
rs4635786	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57267227	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57928386	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58877857	0.83[AFR][1000 genomes]
rs61378184	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532185	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532186	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532187	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532188	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6814056	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6825073	0.82[AFR][1000 genomes]
rs6842093	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72657741	0.82[AFR][1000 genomes]
rs7699596	0.82[AFR][1000 genomes]
rs961386	1.00[YRI][hapmap]

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:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90649400-90696400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:90663400-90691400	Weak transcription	Dnd41	blood
3	chr4:90674600-90682000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:90675000-90680000	Weak transcription	NHLF	lung
5	chr4:90675000-90680200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:90675000-90683800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:90675000-90686200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:90675000-90687000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:90675200-90680000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:90675200-90686000	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:90675200-90687000	Weak transcription	Fetal Kidney	kidney
12	chr4:90675400-90680000	Weak transcription	Hela-S3	cervix
13	chr4:90675400-90687000	Weak transcription	Fetal Brain Male	brain
14	chr4:90675400-90696200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:90675600-90680000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:90676000-90686800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:90676200-90680000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:90676200-90709200	Weak transcription	HUVEC	blood vessel
19	chr4:90678600-90680400	Weak transcription	Fetal Brain Female	brain
20	chr4:90679200-90680800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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