Variant report

Variant	rs1605676
Chromosome Location	chr6:54182231-54182232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1058768	0.86[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs1316576	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1353708	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1508638	0.85[CEU][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1605675	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1813105	0.92[ASN][1000 genomes]
rs1848439	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1848440	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1934791	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995768	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2202802	0.93[CEU][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2221666	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3777652	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3798278	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6458994	0.93[CEU][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs682088	0.85[CEU][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7740868	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7740970	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754752	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7760842	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7766669	0.85[AMR][1000 genomes]
rs9367561	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9367562	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9370290	0.88[ASN][1000 genomes]
rs9382323	0.88[ASN][1000 genomes]
rs9474801	0.90[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1605676	TINAG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54176600-54191800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:54176600-54191800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:54178200-54188400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:54178200-54191600	Weak transcription	Fetal Intestine Large	intestine
5	chr6:54181000-54200400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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