Variant report

Variant	rs3125262
Chromosome Location	chr6:54846337-54846338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1155748	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12191096	0.86[AFR][1000 genomes]
rs12191401	0.86[AFR][1000 genomes]
rs1503138	0.82[EUR][1000 genomes]
rs1503153	0.80[EUR][1000 genomes]
rs1503155	0.83[CEU][hapmap]
rs17678648	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2221335	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs239782	0.85[CEU][hapmap]
rs239784	0.91[CEU][hapmap]
rs239786	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs239795	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs239800	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239803	0.82[EUR][1000 genomes]
rs239804	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239809	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239811	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239814	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs239817	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs239820	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239821	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239822	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2746441	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2746442	0.90[EUR][1000 genomes]
rs3105259	0.86[AFR][1000 genomes]
rs3135456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs376894	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4143677	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4715488	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6459030	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7749067	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7761633	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs869859	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs905460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9357820	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9396004	0.80[EUR][1000 genomes]
rs973206	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs980820	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs995852	1.00[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv5309	chr6:54834971-54855729	Enhancers Active TSS Flanking Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
3	nsv603134	chr6:54841672-54851340	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
4	esv20291	chr6:54846098-54851665	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
5	esv3474002	chr6:54846245-54851547	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
6	esv3474003	chr6:54846291-54851530	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54845000-54847000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:54845400-54846600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:54845400-54847200	Enhancers	HMEC	breast
4	chr6:54845400-54847200	Enhancers	NHEK	skin
5	chr6:54845600-54846800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:54845600-54846800	Enhancers	NHLF	lung
7	chr6:54845600-54847000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:54845800-54847000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:54845800-54847000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:54846000-54846400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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