Variant report

Variant	rs13100559
Chromosome Location	chr3:112529489-112529490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112529420..112531231-chr3:112543770..112545710,2	MCF-7	breast:
2	chr3:112524726..112527255-chr3:112527915..112530520,3	MCF-7	breast:
3	chr3:112358562..112362262-chr3:112527434..112530511,3	MCF-7	breast:
4	chr3:112519716..112521811-chr3:112528431..112531172,2	MCF-7	breast:
5	chr3:112527413..112529549-chr3:112531085..112533830,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction
ENSG00000242770	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10804506	0.95[AFR][1000 genomes]
rs10934188	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1114404	0.82[EUR][1000 genomes]
rs12695270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28782232	0.91[AFR][1000 genomes]
rs6765575	0.91[AFR][1000 genomes]
rs6806976	0.91[AFR][1000 genomes]
rs6808135	0.82[EUR][1000 genomes]
rs7609699	0.89[AFR][1000 genomes]
rs7651207	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9288958	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9288964	0.95[AFR][1000 genomes]
rs9809444	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9810246	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814008	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9823692	0.93[AFR][1000 genomes]
rs9826834	0.95[AFR][1000 genomes]
rs9834599	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9839592	0.93[AFR][1000 genomes]
rs9871326	0.86[AFR][1000 genomes]
rs9871605	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv877343	chr3:112470586-112597706	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112521000-112529800	Weak transcription	A549	lung
2	chr3:112521600-112531600	Weak transcription	Stomach Mucosa	stomach
3	chr3:112526600-112530800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:112527000-112531000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:112527000-112531200	Weak transcription	Primary T cells from cord blood	blood
6	chr3:112527400-112530600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:112527400-112532600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:112527600-112530600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:112527600-112531000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:112528800-112530000	Weak transcription	Aorta	Aorta
11	chr3:112528800-112533600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr3:112529000-112530200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:112529000-112530600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:112529200-112529800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:112529200-112531000	Enhancers	Fetal Kidney	kidney
16	chr3:112529200-112533200	Enhancers	Colon Smooth Muscle	Colon
17	chr3:112529200-112533600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:112529400-112529600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:112529400-112529800	Enhancers	NHDF-Ad	bronchial
20	chr3:112529400-112531200	Enhancers	HSMM	muscle
21	chr3:112529400-112533200	Enhancers	Rectal Smooth Muscle	rectum
22	chr3:112529400-112533200	Enhancers	NHLF	lung
23	chr3:112529400-112533400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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