Variant report

Variant	rs28479904
Chromosome Location	chr15:41268305-41268306
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41265403..41268929-chr15:41273449..41275807,3	MCF-7	breast:
2	chr15:41265160..41268430-chr15:41271742..41276727,5	K562	blood:
3	chr15:41220311..41223112-chr15:41267021..41268787,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128908	Chromatin interaction
ENSG00000128917	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1001341	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1009913	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070314	0.84[EUR][1000 genomes]
rs11070315	0.87[EUR][1000 genomes]
rs11070317	0.88[EUR][1000 genomes]
rs11854472	0.83[EUR][1000 genomes]
rs11855248	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11856572	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12593739	0.84[EUR][1000 genomes]
rs12899590	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905926	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910027	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13329511	0.93[ASN][1000 genomes]
rs1869907	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1962410	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306083	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2412572	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412574	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28473405	0.92[ASN][1000 genomes]
rs28501589	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28538500	0.84[EUR][1000 genomes]
rs28572344	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28581803	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2899002	0.85[EUR][1000 genomes]
rs2925342	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2925343	0.93[ASN][1000 genomes]
rs2925345	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2925346	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2927061	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2927062	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3100807	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3101436	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3214068	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3900905	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3986311	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244584	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4497658	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923890	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924519	0.84[EUR][1000 genomes]
rs4924520	0.84[EUR][1000 genomes]
rs4924521	0.84[EUR][1000 genomes]
rs4924522	0.83[EUR][1000 genomes]
rs4924523	0.83[EUR][1000 genomes]
rs4924524	0.83[EUR][1000 genomes]
rs4924525	0.86[EUR][1000 genomes]
rs4924526	0.84[EUR][1000 genomes]
rs4924528	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924532	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60588038	0.84[EUR][1000 genomes]
rs6492978	0.85[ASN][1000 genomes]
rs7162992	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7169375	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7171437	0.93[ASN][1000 genomes]
rs7174555	0.81[EUR][1000 genomes]
rs7179681	0.81[ASN][1000 genomes]
rs7181816	0.83[EUR][1000 genomes]
rs72735675	0.84[EUR][1000 genomes]
rs72737704	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8023345	0.83[ASN][1000 genomes]
rs8030306	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8042088	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8042127	0.81[EUR][1000 genomes]
rs9796	0.86[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	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1794127	chr15:41245289-41276158	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28479904	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28479904	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41246600-41270000	Weak transcription	HUVEC	blood vessel
2	chr15:41252400-41269400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:41252800-41270800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:41253600-41268800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:41253600-41268800	Weak transcription	Right Ventricle	heart
6	chr15:41258800-41268600	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:41258800-41268800	Weak transcription	Pancreas	Pancrea
8	chr15:41258800-41270400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:41258800-41270800	Weak transcription	Psoas Muscle	Psoas
10	chr15:41258800-41348400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:41259400-41268800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:41260800-41268800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:41261200-41269400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:41261800-41268800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:41262000-41271400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:41264000-41275400	Weak transcription	Fetal Brain Male	brain
17	chr15:41264600-41271800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:41264800-41269600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:41264800-41269800	Weak transcription	K562	blood
20	chr15:41265000-41269200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:41265200-41269200	Weak transcription	HepG2	liver
22	chr15:41265400-41268600	Weak transcription	Esophagus	oesophagus
23	chr15:41265400-41268800	Weak transcription	Hela-S3	cervix
24	chr15:41265400-41269400	Weak transcription	Fetal Lung	lung
25	chr15:41265400-41271600	Weak transcription	Stomach Mucosa	stomach
26	chr15:41266000-41268800	Weak transcription	Primary B cells from cord blood	blood
27	chr15:41266000-41274200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:41266200-41268600	Weak transcription	Brain Angular Gyrus	brain
29	chr15:41266200-41275000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr15:41266400-41268600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:41266400-41268600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:41266600-41268800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:41266600-41274000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:41266600-41275000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:41266800-41268600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:41266800-41273800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr15:41266800-41274000	Strong transcription	Osteobl	bone
38	chr15:41266800-41275200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:41266800-41277400	Strong transcription	Fetal Muscle Leg	muscle
40	chr15:41266800-41278400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:41266800-41280200	Strong transcription	Fetal Brain Female	brain
42	chr15:41266800-41280400	Strong transcription	Brain Substantia Nigra	brain
43	chr15:41266800-41281400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr15:41266800-41283800	Strong transcription	A549	lung
45	chr15:41266800-41290000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:41266800-41298400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:41267000-41268800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:41267000-41270000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:41267000-41280600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:41267000-41280800	Strong transcription	Brain Germinal Matrix	brain

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