Variant report

Variant	rs28576457
Chromosome Location	chr15:41713444-41713445
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41693298..41696074-chr15:41713088..41714637,2	MCF-7	breast:
2	chr15:41708317..41710602-chr15:41711098..41714425,3	MCF-7	breast:
3	chr15:41706897..41710806-chr15:41711426..41714664,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137806	Chromatin interaction
ENSG00000137815	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10518717	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070328	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	1.00[ASN][1000 genomes]
rs11630656	1.00[ASN][1000 genomes]
rs11630799	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11635906	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854081	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757468	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730589	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	1.00[ASN][1000 genomes]
rs2730056	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377562	1.00[ASN][1000 genomes]
rs28416360	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28421136	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	1.00[ASN][1000 genomes]
rs28456082	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458941	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459164	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28463309	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493702	1.00[ASN][1000 genomes]
rs28535540	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555198	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	1.00[ASN][1000 genomes]
rs28584379	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673484	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	1.00[ASN][1000 genomes]
rs28700583	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703570	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	1.00[ASN][1000 genomes]
rs28716689	1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316606	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316607	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316611	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316616	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204853	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34040639	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34285452	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34665396	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55725658	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56341337	0.83[EUR][1000 genomes]
rs56400990	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	1.00[ASN][1000 genomes]
rs6493000	1.00[ASN][1000 genomes]
rs6493003	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162231	1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7164211	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164684	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	1.00[ASN][1000 genomes]
rs7165914	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	1.00[ASN][1000 genomes]
rs7168431	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	1.00[ASN][1000 genomes]
rs72737786	1.00[ASN][1000 genomes]
rs72737792	1.00[ASN][1000 genomes]
rs72737793	1.00[ASN][1000 genomes]
rs72739630	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	1.00[ASN][1000 genomes]
rs8034840	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	1.00[ASN][1000 genomes]
rs8038132	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041809	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs9568	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
5	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
6	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv569232	chr15:41694377-41730246	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs28576457	NDUFAF1	cis	lung	GTEx
rs28576457	NDUFAF1	cis	Whole Blood	GTEx
rs28576457	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs28576457	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs28576457	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28576457	OIP5-AS1	cis	Nerve Tibial	GTEx
rs28576457	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28576457	OIP5-AS1	cis	Artery Tibial	GTEx
rs28576457	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs28576457	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28576457	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28576457	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28576457	NDUFAF1	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41710400-41715600	Weak transcription	Lung	lung
2	chr15:41710400-41724600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:41710400-41745200	Weak transcription	Esophagus	oesophagus
4	chr15:41710400-41750000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:41710600-41714600	Weak transcription	Stomach Mucosa	stomach
6	chr15:41710600-41715000	Weak transcription	Ovary	ovary
7	chr15:41710600-41716200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:41710600-41717000	Weak transcription	Fetal Stomach	stomach
9	chr15:41710600-41721200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:41710600-41721200	Weak transcription	Right Atrium	heart
11	chr15:41710600-41723800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:41710600-41723800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:41710600-41729800	Weak transcription	Brain Substantia Nigra	brain
14	chr15:41710600-41731600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:41710600-41731600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:41710600-41731800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:41710600-41733600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:41710600-41745200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:41710800-41716200	Weak transcription	Fetal Brain Female	brain
20	chr15:41710800-41716400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:41710800-41718800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:41710800-41718800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:41710800-41718800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:41710800-41718800	Weak transcription	HMEC	breast
25	chr15:41710800-41718800	Weak transcription	NH-A	brain
26	chr15:41710800-41718800	Weak transcription	NHLF	lung
27	chr15:41710800-41720800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:41710800-41720800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr15:41710800-41721200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:41710800-41724200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:41710800-41724800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:41710800-41724800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:41710800-41726600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:41710800-41727800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:41710800-41729800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:41710800-41729800	Weak transcription	Psoas Muscle	Psoas
37	chr15:41710800-41730200	Weak transcription	Fetal Intestine Large	intestine
38	chr15:41710800-41730600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:41710800-41731600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:41710800-41731800	Weak transcription	Left Ventricle	heart
41	chr15:41710800-41733400	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:41710800-41733400	Weak transcription	HSMMtube	muscle
43	chr15:41711000-41714200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:41711000-41718800	Weak transcription	HSMM	muscle
45	chr15:41711000-41729800	Weak transcription	Placenta	Placenta
46	chr15:41711000-41730200	Weak transcription	Adipose Nuclei	Adipose
47	chr15:41711000-41730600	Weak transcription	Osteobl	bone
48	chr15:41711200-41715400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:41711200-41718800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr15:41711200-41721200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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