Variant report

Variant	rs6998307
Chromosome Location	chr8:61368722-61368723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61357506..61359309-chr8:61366924..61369174,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10087760	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10092773	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10102945	0.88[ASN][1000 genomes]
rs10504312	0.87[ASN][1000 genomes]
rs11988766	0.87[ASN][1000 genomes]
rs11988798	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12548711	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1318227	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1552070	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1842388	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1893277	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1893279	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1941467	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2012856	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2068587	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2155831	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6471877	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6471880	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6471881	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6982032	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6986664	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6993588	0.82[EUR][1000 genomes]
rs6994192	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6999822	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7004236	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7814226	0.88[ASN][1000 genomes]
rs7819947	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7824474	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7824671	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7828383	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7831106	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7841648	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9785091	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv971314	chr8:61359401-61436209	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6998307	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs6998307	RP11-163N6.2	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61366800-61369400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:61366800-61369400	Enhancers	HMEC	breast
3	chr8:61366800-61369600	Enhancers	NHEK	skin
4	chr8:61367000-61369600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:61367200-61369200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:61367400-61369200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr8:61367600-61368800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr8:61367600-61369400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr8:61367800-61369000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr8:61367800-61369600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr8:61367800-61369600	Enhancers	A549	lung
12	chr8:61368600-61371400	Weak transcription	NHLF	lung

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