Variant report

Variant	rs28559992
Chromosome Location	chr12:29416641-29416642
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11050164	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050165	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050166	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050172	0.89[ASN][1000 genomes]
rs11050211	0.89[ASN][1000 genomes]
rs12301257	0.89[ASN][1000 genomes]
rs12301468	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12304675	0.89[ASN][1000 genomes]
rs12314513	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316548	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319953	0.89[ASN][1000 genomes]
rs12322493	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16934110	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs766764	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3501674	chr12:29416561-29416660	Weak transcription	n/a	n/a	inside rSNPs	diseases
5	esv3423898	chr12:29416571-29416669	Weak transcription	n/a	n/a	inside rSNPs	diseases
6	esv3501685	chr12:29416576-29416664	Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29408200-29423200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:29408200-29425800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:29408400-29424000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr12:29410000-29421000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:29410000-29425800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:29410000-29426200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:29414000-29416800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:29414000-29423400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:29414200-29422800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:29414400-29434000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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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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