Variant report

Variant	rs73139180
Chromosome Location	chr3:115772246-115772247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:115771673-115772413	H1-neurons	neurons:	n/a	n/a
2	ELF1	chr3:115772143-115772304	K562	blood:	n/a	chr3:115772213-115772226 chr3:115772176-115772187
3	CTCF	chr3:115772100-115772250	HPF	lung:	n/a	n/a
4	POLR2A	chr3:115771752-115772288	H1-neurons	neurons:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:73159068..73161464-chr3:115770665..115773645,3	MCF-7	breast:
2	chr11:62608645..62609195-chr3:115772145..115772665,4	HCT-116	colon:
3	chr11:62608624..62609620-chr3:115772145..115772665,2	NB4	blood:
4	chr10:103124108..103124631-chr3:115772145..115772665,2	HCT-116	colon:
5	chr11:62607723..62610629-chr3:115772165..115773665,2	K562	blood:
6	chr11:62608633..62609155-chr3:115772145..115772665,2	Hela-S3	cervix:
7	chr11:62607697..62610629-chr3:115772145..115773665,2	K562	blood:
8	chr17:41464664..41466373-chr3:115770665..115773645,2	MCF-7	breast:
9	chr17:41399462..41401706-chr3:115772145..115773645,2	MCF-7	breast:
10	chr17:41464397..41466181-chr3:115772145..115773645,2	MCF-7	breast:
11	chr11:62608648..62609195-chr3:115772145..115772665,2	MCF-7	breast:
12	chr3:73160073..73160628-chr3:115771645..115772645,4	HCT-116	colon:
13	chr17:41463814..41467387-chr3:115770645..115773645,5	K562	blood:

No data

No data

No data

Variant related genes	Relation type
LSAMP	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000223247	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10439991	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934317	0.81[ASN][1000 genomes]
rs12493033	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1920386	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4629329	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55813816	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55851212	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6778817	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73139170	0.85[ASN][1000 genomes]
rs73139177	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73139184	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139188	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7432754	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7630438	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289038	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9859789	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931948	chr3:114884574-115802562	Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2760762	chr3:115476222-115807650	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv829685	chr3:115643521-115812913	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2756413	chr3:115721898-115908480	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1001538	chr3:115746561-115791116	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv2751975	chr3:115766285-115902901	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115758000-115772800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:115759000-115778200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:115766000-115774000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:115766000-115775800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:115766200-115794200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:115770400-115775800	Weak transcription	HMEC	breast
7	chr3:115770400-115777000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:115770600-115774400	Weak transcription	GM12878-XiMat	blood
9	chr3:115770800-115772800	Weak transcription	Brain Angular Gyrus	brain
10	chr3:115771000-115773800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:115771600-115773800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:115772000-115772800	Weak transcription	Brain Substantia Nigra	brain

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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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