Variant report

Variant	rs3822894
Chromosome Location	chr6:54231488-54231489
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:44)

rs_ID	r²[population]
rs10080851	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1508634	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1508635	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17755505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17828461	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17828521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736352	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3736353	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777636	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3777646	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41413844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55868486	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56257351	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57614124	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57677324	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58204168	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58555206	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58969244	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59502546	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60299436	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61162221	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67321849	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6902402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6907037	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6926710	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6927886	0.87[EUR][1000 genomes]
rs72959309	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72965255	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7739948	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7746042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758586	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs7763022	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7767253	0.81[ASN][1000 genomes]
rs9395950	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9464067	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9464068	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9464069	0.87[ASN][1000 genomes]
rs9474815	0.82[JPT][hapmap]
rs9474821	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9474829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9474831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs949469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54211800-54256200	Weak transcription	Fetal Intestine Large	intestine
2	chr6:54212000-54257400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:54227200-54231600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:54227200-54231800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:54231400-54232400	Enhancers	NHEK	skin
6	chr6:54231400-54232400	Enhancers	Osteobl	bone
7	chr6:54231400-54232600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:54231400-54232600	Enhancers	HMEC	breast
9	chr6:54231400-54232800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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