Variant report

Variant	rs2746441
Chromosome Location	chr6:54758069-54758070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1155748	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1503138	0.87[EUR][1000 genomes]
rs1503153	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1503155	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs17678648	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2221335	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs239784	0.84[CEU][hapmap];0.85[YRI][hapmap]
rs239786	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239795	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239800	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs239803	0.87[EUR][1000 genomes]
rs239804	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs239809	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs239811	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs239814	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239817	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239820	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs239821	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs239822	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2746442	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3125262	0.90[EUR][1000 genomes]
rs3135456	0.90[EUR][1000 genomes]
rs376894	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4143677	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4715488	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6459030	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7749067	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7761633	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs869859	0.90[EUR][1000 genomes]
rs905460	0.90[EUR][1000 genomes]
rs9357820	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs9367595	0.83[EUR][1000 genomes]
rs9396004	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs973206	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs980820	0.90[EUR][1000 genomes]
rs995852	1.00[CEU][hapmap];0.87[EUR][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	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	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
2	chr6:54744400-54761000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:54752200-54759000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:54752400-54758600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:54756200-54758400	Enhancers	HMEC	breast
6	chr6:54757200-54763000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:54757800-54760600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:54757800-54763200	Weak transcription	NHEK	skin
9	chr6:54758000-54761200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:54758000-54769400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:54758000-54775000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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