Variant report

Variant	rs72804469
Chromosome Location	chr2:47053372-47053373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:47053228-47054300	U87	brain:	n/a	n/a
2	POLR2A	chr2:47053182-47055198	U87	brain:	n/a	n/a
3	POLR2A	chr2:47053099-47055204	U87	brain:	n/a	n/a
4	RAD21	chr2:47053276-47053659	IMR90	lung:	n/a	chr2:47053418-47053430 chr2:47053357-47053369 chr2:47053420-47053430
5	CEBPB	chr2:47053298-47053673	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47052966..47054812-chr2:47054856..47057996,3	MCF-7	breast:
2	chr2:47051846..47053973-chr2:47059703..47062442,2	MCF-7	breast:

Variant related genes	Relation type
LINC01119	TF binding region
ENSG00000239332	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17035709	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17824594	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55980660	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56060227	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56172110	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58979440	0.90[ASN][1000 genomes]
rs72804436	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72804437	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72804438	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72804445	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72804446	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72804450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72804451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72804452	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72804458	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72804470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv817840	chr2:47044218-47070827	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47039800-47053800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:47042800-47053400	Weak transcription	Fetal Lung	lung
3	chr2:47045200-47054800	Weak transcription	Spleen	Spleen
4	chr2:47049200-47053800	Weak transcription	Lung	lung
5	chr2:47049600-47054000	Weak transcription	Left Ventricle	heart
6	chr2:47049600-47054600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:47050000-47054400	Weak transcription	Fetal Heart	heart
8	chr2:47051200-47057200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:47051800-47059600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:47052000-47054600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:47052000-47055400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:47052200-47053800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:47052200-47054400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:47052200-47055200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:47052200-47056400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:47052400-47054400	Weak transcription	HMEC	breast
17	chr2:47052800-47054600	Enhancers	Osteobl	bone
18	chr2:47052800-47055400	Enhancers	NH-A	brain
19	chr2:47053000-47053600	Enhancers	Placenta	Placenta
20	chr2:47053000-47054200	Enhancers	Right Atrium	heart
21	chr2:47053000-47055000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:47053000-47055000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr2:47053000-47055000	Enhancers	NHDF-Ad	bronchial
24	chr2:47053000-47055000	Enhancers	NHLF	lung
25	chr2:47053000-47060000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:47053200-47053400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:47053200-47055400	Enhancers	Right Ventricle	heart

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