Variant report

Variant	rs527680
Chromosome Location	chr13:96746789-96746790
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	chr13:96746204..96748627-chr13:96759326..96761567,2	K562	blood:
2	chr13:96742136..96745093-chr13:96745710..96749821,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185352	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1980942	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1996054	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2389530	0.80[CEU][hapmap]
rs2774113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2849438	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs472788	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs473930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs485648	0.84[EUR][1000 genomes]
rs493109	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs506474	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs509572	0.88[CEU][hapmap]
rs517173	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs521235	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs527096	0.83[EUR][1000 genomes]
rs529306	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs531090	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs532399	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs535812	0.84[EUR][1000 genomes]
rs536606	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs537571	0.82[EUR][1000 genomes]
rs539604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs541811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs544080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs551457	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs552598	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs561996	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs576184	0.88[CEU][hapmap]
rs590758	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs592205	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs595696	0.89[CEU][hapmap]
rs6492826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7993804	0.93[EUR][1000 genomes]
rs816139	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs9516640	0.92[EUR][1000 genomes]
rs9525085	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9525095	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs9525098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv900936	chr13:96697209-97032483	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs527680	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs527680	UGGT2	cis	Muscle Skeletal	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96744400-96752800	Weak transcription	Aorta	Aorta
2	chr13:96746000-96747000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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