Variant report

Variant	rs28380723
Chromosome Location	chr12:121396646-121396647
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:9)

rs_ID	r²[population]
rs11065360	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065361	0.98[ASN][1000 genomes]
rs12815613	0.98[ASN][1000 genomes]
rs12826999	0.98[ASN][1000 genomes]
rs55913575	0.98[ASN][1000 genomes]
rs66627474	0.98[ASN][1000 genomes]
rs73226265	0.97[ASN][1000 genomes]
rs7961554	0.98[ASN][1000 genomes]
rs9669493	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1838192	chr12:121363589-121402932	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	esv3498641	chr12:121395975-121396765	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3498652	chr12:121395975-121396765	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28380723	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121393000-121399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:121393600-121397200	Enhancers	Fetal Intestine Small	intestine
3	chr12:121393600-121400600	Enhancers	Fetal Intestine Large	intestine
4	chr12:121393800-121397200	Enhancers	HepG2	liver
5	chr12:121394000-121396800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:121394600-121398800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:121394600-121408200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:121394800-121397400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr12:121395200-121396800	Weak transcription	A549	lung
10	chr12:121395200-121396800	Weak transcription	K562	blood
11	chr12:121395600-121397600	Enhancers	Colonic Mucosa	Colon
12	chr12:121395800-121408200	Weak transcription	Fetal Kidney	kidney
13	chr12:121396200-121397200	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr12:121396200-121399800	Enhancers	Fetal Thymus	thymus
15	chr12:121396600-121399000	Enhancers	Thymus	Thymus
16	chr12:121396600-121400600	Enhancers	Duodenum Mucosa	Duodenum

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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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