Variant report

Variant	rs58151706
Chromosome Location	chr4:57298562-57298563
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57278722..57280888-chr4:57296778..57299271,2	MCF-7	breast:
2	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
3	chr4:57250870..57256080-chr4:57298204..57304153,16	K562	blood:
4	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
5	chr4:57250870..57256510-chr4:57298204..57303491,14	K562	blood:
6	chr4:57297760..57299581-chr4:57396785..57398752,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269921	Chromatin interaction
ENSG00000270109	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000157426	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10008223	0.92[ASN][1000 genomes]
rs10013402	0.94[ASN][1000 genomes]
rs10017460	0.93[ASN][1000 genomes]
rs10051	0.80[ASN][1000 genomes]
rs10434444	0.95[ASN][1000 genomes]
rs10434445	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10461357	0.82[ASN][1000 genomes]
rs1060472	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133442	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1124569	0.85[ASN][1000 genomes]
rs12498340	0.90[ASN][1000 genomes]
rs12501334	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12501502	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12503412	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12504291	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12505939	0.80[ASN][1000 genomes]
rs12508008	0.82[ASN][1000 genomes]
rs12509542	0.82[ASN][1000 genomes]
rs12510712	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12511770	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12513091	0.82[ASN][1000 genomes]
rs12646890	0.82[ASN][1000 genomes]
rs14211	0.80[ASN][1000 genomes]
rs1474179	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1520026	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1520030	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17086696	0.94[ASN][1000 genomes]
rs17086794	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17086853	0.82[ASN][1000 genomes]
rs1967559	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1983378	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2030366	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2271923	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28510634	0.92[ASN][1000 genomes]
rs28866881	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796541	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4263445	0.85[ASN][1000 genomes]
rs4340842	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4346704	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4493603	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4618376	0.82[ASN][1000 genomes]
rs4864579	0.94[ASN][1000 genomes]
rs4864580	0.94[ASN][1000 genomes]
rs4864583	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865088	0.85[ASN][1000 genomes]
rs4865089	0.86[ASN][1000 genomes]
rs4865092	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4865103	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4865107	0.82[ASN][1000 genomes]
rs4865108	0.80[ASN][1000 genomes]
rs5010012	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55915354	0.80[ASN][1000 genomes]
rs56040009	0.80[ASN][1000 genomes]
rs56099714	0.82[ASN][1000 genomes]
rs56392224	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56887793	0.96[ASN][1000 genomes]
rs61032900	0.85[ASN][1000 genomes]
rs6554358	0.80[ASN][1000 genomes]
rs66810706	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66858948	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs66863699	0.82[ASN][1000 genomes]
rs67957495	0.85[ASN][1000 genomes]
rs6820279	0.85[ASN][1000 genomes]
rs6820314	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6821301	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6829250	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6832797	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6834696	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6846895	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6849183	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6855041	0.86[EUR][1000 genomes]
rs7664841	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7670991	0.90[ASN][1000 genomes]
rs8340	0.88[ASN][1000 genomes]
rs9799864	0.83[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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58151706	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs58151706	SRP72	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
4	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
5	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:57277000-57299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:57277000-57300000	Weak transcription	HSMM	muscle
8	chr4:57278000-57299200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:57278200-57300200	Weak transcription	Fetal Kidney	kidney
10	chr4:57278200-57300200	Weak transcription	NHDF-Ad	bronchial
11	chr4:57280800-57299400	Weak transcription	Fetal Lung	lung
12	chr4:57281000-57299200	Weak transcription	HMEC	breast
13	chr4:57284800-57300400	Weak transcription	Fetal Intestine Small	intestine
14	chr4:57287800-57299200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:57288000-57299200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:57289600-57299800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:57292000-57299200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:57292200-57299200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:57292200-57299200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:57292200-57299200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:57292200-57299800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:57293400-57298800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:57293400-57299200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr4:57294000-57299200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:57295000-57299200	Enhancers	HepG2	liver
26	chr4:57295000-57305000	Active TSS	GM12878-XiMat	blood
27	chr4:57295400-57300000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:57296400-57299400	Weak transcription	HUVEC	blood vessel
29	chr4:57296600-57298600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:57296600-57300400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:57297200-57300000	Weak transcription	Fetal Brain Male	brain
32	chr4:57298000-57299400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:57298200-57299200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:57298200-57299200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:57298200-57299200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:57298200-57299200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:57298200-57299200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:57298200-57299200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:57298200-57299200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:57298200-57299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:57298200-57299200	Enhancers	Dnd41	blood
42	chr4:57298200-57299600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr4:57298200-57299600	Weak transcription	NHEK	skin
44	chr4:57298200-57299800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:57298400-57299200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:57298400-57299200	Weak transcription	K562	blood
47	chr4:57298400-57299400	Weak transcription	A549	lung
48	chr4:57298400-57299600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:57298400-57300400	Weak transcription	Brain Germinal Matrix	brain
50	chr4:57298400-57305600	Active TSS	Hela-S3	cervix

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