Variant report

Variant	rs58939003
Chromosome Location	chr3:118924010-118924011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:118916389..118918845-chr3:118921672..118924388,2	MCF-7	breast:
2	chr3:118922153..118924777-chr3:118944047..118945599,2	K562	blood:
3	chr3:118902403..118905431-chr3:118923096..118925754,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240254	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10511382	0.91[EUR][1000 genomes]
rs11927939	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12634868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081519	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16829477	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3796356	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796357	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4370022	0.91[EUR][1000 genomes]
rs4687840	0.91[EUR][1000 genomes]
rs4687980	0.87[EUR][1000 genomes]
rs4687981	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4687982	0.91[EUR][1000 genomes]
rs57258193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61162364	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6438502	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7426444	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9840317	0.87[EUR][1000 genomes];0.92[ASN][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv591362	chr3:118906442-118948155	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118901000-118924200	Weak transcription	Pancreas	Pancrea
2	chr3:118903400-118924200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:118904600-118936400	Weak transcription	Gastric	stomach
4	chr3:118908400-118928200	Weak transcription	Fetal Stomach	stomach
5	chr3:118911800-118932600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:118915000-118925200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:118915200-118928400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:118915200-118934800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:118917800-118925200	Weak transcription	Left Ventricle	heart
10	chr3:118919000-118925600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:118920400-118930400	Weak transcription	Fetal Kidney	kidney
12	chr3:118921000-118928000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:118921400-118931200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:118922200-118927400	Weak transcription	HSMM	muscle
15	chr3:118922600-118924600	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr3:118922600-118925400	Weak transcription	Lung	lung
17	chr3:118922600-118929000	Weak transcription	Spleen	Spleen
18	chr3:118922800-118926200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr3:118922800-118926200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:118923000-118927600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr3:118923000-118929000	Weak transcription	Brain Germinal Matrix	brain
22	chr3:118923200-118924600	Enhancers	HepG2	liver
23	chr3:118923200-118925200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:118923200-118927400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:118923400-118924200	Weak transcription	K562	blood
26	chr3:118923400-118926800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:118923400-118927000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:118923400-118927400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:118923600-118924800	Enhancers	Fetal Muscle Leg	muscle
30	chr3:118923600-118926000	Flanking Active TSS	A549	lung
31	chr3:118923600-118930800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:118923800-118924200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:118923800-118924400	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr3:118923800-118924600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:118923800-118931600	Enhancers	Stomach Mucosa	stomach
36	chr3:118924000-118924200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr3:118924000-118924200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:118924000-118924200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:118924000-118924200	Enhancers	Fetal Muscle Trunk	muscle
40	chr3:118924000-118924200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr3:118924000-118924200	Enhancers	NHDF-Ad	bronchial
42	chr3:118924000-118924200	Enhancers	NHEK	skin
43	chr3:118924000-118924400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr3:118924000-118924400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:118924000-118924400	Enhancers	Aorta	Aorta
46	chr3:118924000-118924400	Flanking Active TSS	Osteobl	bone

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