Variant report

Variant	rs1085093
Chromosome Location	chr1:84761348-84761349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12125649	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12135562	1.00[ASN][1000 genomes]
rs12142220	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1246574	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316636	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316641	1.00[ASN][1000 genomes]
rs316643	0.81[EUR][1000 genomes]
rs316689	1.00[ASN][1000 genomes]
rs72942037	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs784828	1.00[CHB][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs784830	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs784831	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs784832	0.83[EUR][1000 genomes]
rs784833	0.83[EUR][1000 genomes]
rs813056	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs868612	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[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	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Metabolic syndrome	20694148	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84744000-84763200	Weak transcription	Gastric	stomach
2	chr1:84753800-84764000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:84757200-84761400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:84758000-84763800	Weak transcription	NHLF	lung
5	chr1:84760200-84761400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:84760400-84761800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
7	chr1:84760400-84763200	Weak transcription	Fetal Thymus	thymus
8	chr1:84760800-84762800	Weak transcription	Primary T cells from cord blood	blood
9	chr1:84761000-84761800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
10	chr1:84761200-84762600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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