Variant report

Variant	rs239779
Chromosome Location	chr6:54757531-54757532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10948879	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12208341	0.82[AMR][1000 genomes]
rs12208348	0.82[AMR][1000 genomes]
rs12211168	0.81[AMR][1000 genomes]
rs148109	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs171224	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs181155	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2134539	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2143798	0.80[ASN][1000 genomes]
rs2179786	0.80[ASN][1000 genomes]
rs2207025	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2207026	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs239781	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs239783	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs239790	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs239792	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs239794	0.82[EUR][1000 genomes]
rs239796	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs239801	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs239813	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs239815	0.81[EUR][1000 genomes]
rs239837	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs239850	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239854	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2746443	0.82[EUR][1000 genomes]
rs2816810	0.83[EUR][1000 genomes]
rs2816811	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2816812	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3996950	0.80[EUR][1000 genomes]
rs421957	0.82[EUR][1000 genomes]
rs6459034	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7741915	0.89[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	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:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
2	chr6:54744200-54757600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:54744400-54761000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:54746400-54757800	Weak transcription	Hela-S3	cervix
5	chr6:54752200-54759000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:54752400-54758600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:54755800-54758000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:54755800-54758000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:54756200-54758400	Enhancers	HMEC	breast
10	chr6:54757000-54757800	Enhancers	NHEK	skin
11	chr6:54757200-54757600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:54757200-54763000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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