Variant report

Variant	rs58889726
Chromosome Location	chr5:127870933-127870934
allele	G/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	FOXM1	chr5:127870232-127870970	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr5:127870141-127870955	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr5:127870296-127870995	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr5:127870311-127870946	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr5:127870371-127870985	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SLC27A6	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10039900	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10040056	0.82[EUR][1000 genomes]
rs10042096	0.95[ASN][1000 genomes]
rs10053025	0.95[ASN][1000 genomes]
rs10062344	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10063362	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10063961	0.84[EUR][1000 genomes]
rs10477685	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10478812	0.91[ASN][1000 genomes]
rs10478813	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10478814	0.95[ASN][1000 genomes]
rs11960575	0.91[ASN][1000 genomes]
rs17164094	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17164113	0.95[ASN][1000 genomes]
rs17839642	0.89[ASN][1000 genomes]
rs1897998	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55721088	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55735252	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56049336	0.91[ASN][1000 genomes]
rs57050667	0.95[ASN][1000 genomes]
rs59674940	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60201468	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60571728	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60975118	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6595830	0.95[ASN][1000 genomes]
rs6595831	0.95[ASN][1000 genomes]
rs6595834	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6595836	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595837	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595841	0.84[EUR][1000 genomes]
rs6595842	0.84[EUR][1000 genomes]
rs6860199	0.95[ASN][1000 genomes]
rs6864057	0.92[ASN][1000 genomes]
rs6886186	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6887851	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6892484	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6893116	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6893181	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6893248	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6893301	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73346331	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73784600	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73787623	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73787627	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs768744	0.94[ASN][1000 genomes]
rs7703313	0.91[ASN][1000 genomes]
rs7708713	0.95[ASN][1000 genomes]
rs7713044	0.95[ASN][1000 genomes]
rs7722917	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722950	0.95[ASN][1000 genomes]
rs7723500	0.95[ASN][1000 genomes]
rs7725740	0.95[ASN][1000 genomes]
rs7726535	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9327478	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs981411	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv2763497	chr5:127745955-127882468	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv530822	chr5:127777365-127900742	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv427734	chr5:127805281-128088632	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1019560	chr5:127814656-127873680	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv537895	chr5:127814656-127873680	ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127840200-127872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:127853200-127872400	Weak transcription	Osteobl	bone
3	chr5:127854000-127872000	Weak transcription	Ovary	ovary
4	chr5:127855000-127871200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:127861000-127871000	Weak transcription	A549	lung
6	chr5:127861000-127871800	Weak transcription	Fetal Lung	lung
7	chr5:127862600-127872000	Weak transcription	NHLF	lung
8	chr5:127863200-127872000	Weak transcription	HUVEC	blood vessel
9	chr5:127863600-127872000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:127864600-127871800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:127866400-127871000	Weak transcription	HMEC	breast
12	chr5:127867200-127871800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:127868400-127871800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:127868600-127871800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:127868800-127871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:127869200-127871600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:127869200-127871800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr5:127869200-127871800	Weak transcription	Right Ventricle	heart
19	chr5:127869200-127872000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:127869200-127875000	Active TSS	Fetal Heart	heart
21	chr5:127870000-127871000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:127870400-127871000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:127870400-127871000	Active TSS	Fetal Kidney	kidney
24	chr5:127870400-127871200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:127870400-127871200	Enhancers	Fetal Muscle Leg	muscle
26	chr5:127870400-127871400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:127870400-127871800	Active TSS	NHDF-Ad	bronchial
28	chr5:127870400-127872200	Active TSS	Placenta	Placenta
29	chr5:127870400-127872400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:127870600-127871000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:127870600-127871600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:127870600-127871800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr5:127870800-127871000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:127870800-127871000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr5:127870800-127871000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr5:127870800-127871000	Enhancers	NHEK	skin
37	chr5:127870800-127871800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:127870800-127871800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:127870800-127871800	Weak transcription	Left Ventricle	heart
40	chr5:127870800-127871800	Enhancers	NH-A	brain
41	chr5:127870800-127872000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:127870800-127872000	Active TSS	Fetal Stomach	stomach
43	chr5:127870800-127872000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr5:127870800-127875200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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