Variant report

Variant	rs1983561
Chromosome Location	chr6:5584936-5584937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12202026	0.96[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2142737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4960103	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4960104	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4960105	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4960109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4960110	0.83[CHB][hapmap];0.80[LWK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs6597145	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs742114	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7756622	0.83[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7757733	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9405275	0.91[CHB][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9502319	0.83[CHB][hapmap]
rs9504439	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1016905	chr6:5566364-5639167	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5577400-5639800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5581000-5614200	Weak transcription	Lung	lung
3	chr6:5581000-5640400	Weak transcription	Gastric	stomach
4	chr6:5582000-5586600	Weak transcription	Primary B cells from cord blood	blood
5	chr6:5582200-5595000	Weak transcription	Fetal Stomach	stomach
6	chr6:5583400-5585400	Enhancers	NHDF-Ad	bronchial
7	chr6:5584000-5585000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:5584000-5585000	Enhancers	HSMMtube	muscle
9	chr6:5584000-5585200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:5584000-5585200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr6:5584000-5585200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:5584000-5585200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:5584000-5585200	Enhancers	Brain Substantia Nigra	brain
14	chr6:5584000-5585200	Enhancers	HSMM	muscle
15	chr6:5584200-5585200	Enhancers	NH-A	brain
16	chr6:5584200-5585200	Enhancers	NHLF	lung
17	chr6:5584200-5585400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:5584400-5585200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr6:5584400-5585400	Enhancers	Brain Hippocampus Middle	brain
20	chr6:5584600-5585200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:5584600-5589000	Weak transcription	Fetal Heart	heart
22	chr6:5584600-5589400	Weak transcription	Fetal Lung	lung
23	chr6:5584800-5585200	Enhancers	Osteobl	bone

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