Variant report

Variant	rs16928547
Chromosome Location	chr10:28443371-28443372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16928528	1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs16928532	1.00[MEX][hapmap];0.84[MKK][hapmap];0.83[AMR][1000 genomes]
rs16928549	0.86[AFR][1000 genomes]
rs41306320	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73606080	1.00[AMR][1000 genomes]
rs73606081	0.83[AMR][1000 genomes]
rs73606083	1.00[AMR][1000 genomes]
rs73608039	1.00[AMR][1000 genomes]
rs73608040	0.83[AMR][1000 genomes]
rs73608041	1.00[AMR][1000 genomes]
rs73608048	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831816	chr10:28304698-28493635	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv831817	chr10:28369836-28539930	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1848511	chr10:28373644-28464753	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv894989	chr10:28384098-28449974	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv949151	chr10:28386125-28455221	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
11	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16928547	FAM153A	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28417000-28449200	Weak transcription	Pancreas	Pancrea
2	chr10:28417600-28458000	Weak transcription	Aorta	Aorta
3	chr10:28427200-28448600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr10:28434800-28446200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr10:28436800-28447200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr10:28436800-28451800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr10:28437200-28446600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr10:28439000-28447800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr10:28439000-28452800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr10:28439000-28466600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr10:28439000-28467000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr10:28439200-28446600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:28439200-28466600	Weak transcription	Primary T cells from cord blood	blood
14	chr10:28439600-28452000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr10:28443000-28443800	Enhancers	Colon Smooth Muscle	Colon
16	chr10:28443200-28443400	Enhancers	Stomach Smooth Muscle	stomach

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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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