Variant report

Variant	rs12899590
Chromosome Location	chr15:41267697-41267698
allele	A/G
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	chr15:41231932..41234904-chr15:41266157..41268211,2	K562	blood:
3	chr15:41265160..41268430-chr15:41271742..41276727,5	K562	blood:
4	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: 1 )

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

rs_ID	r²[population]
rs1001341	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1009913	0.84[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	0.82[EUR][1000 genomes]
rs11855248	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11856572	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12593739	0.84[EUR][1000 genomes]
rs12905926	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910027	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13329511	0.93[ASN][1000 genomes]
rs1869907	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1962410	0.84[ASN][1000 genomes]
rs2306083	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2412572	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412574	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28473405	0.92[ASN][1000 genomes]
rs28479904	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28501589	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28538500	0.84[EUR][1000 genomes]
rs28572344	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28581803	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2899002	0.85[EUR][1000 genomes]
rs2925342	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2925343	0.93[ASN][1000 genomes]
rs2925345	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2925346	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2927061	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2927062	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3100807	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3101436	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3214068	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3900905	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3986311	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244584	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4497658	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923890	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924519	0.87[EUR][1000 genomes]
rs4924520	0.84[EUR][1000 genomes]
rs4924521	0.84[EUR][1000 genomes]
rs4924522	0.86[EUR][1000 genomes]
rs4924523	0.83[EUR][1000 genomes]
rs4924524	0.83[EUR][1000 genomes]
rs4924525	0.89[EUR][1000 genomes]
rs4924526	0.84[EUR][1000 genomes]
rs4924528	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924532	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60588038	0.84[EUR][1000 genomes]
rs6492978	0.85[ASN][1000 genomes]
rs7162992	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7169375	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7171437	0.93[ASN][1000 genomes]
rs7174555	0.81[EUR][1000 genomes]
rs7179681	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7181816	0.82[EUR][1000 genomes]
rs72735675	0.84[EUR][1000 genomes]
rs72737704	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8023345	0.83[ASN][1000 genomes]
rs8030306	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8042088	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8042127	0.81[EUR][1000 genomes]
rs9796	0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12899590	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41246400-41268200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:41246600-41270000	Weak transcription	HUVEC	blood vessel
3	chr15:41246800-41268000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr15:41246800-41268200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:41249400-41268000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:41252400-41269400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:41252800-41270800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:41253600-41268200	Weak transcription	Spleen	Spleen
9	chr15:41253600-41268800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:41253600-41268800	Weak transcription	Right Ventricle	heart
11	chr15:41258600-41268000	Weak transcription	Fetal Intestine Small	intestine
12	chr15:41258800-41267800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:41258800-41267800	Weak transcription	Lung	lung
14	chr15:41258800-41267800	Weak transcription	Ovary	ovary
15	chr15:41258800-41268000	Weak transcription	Colonic Mucosa	Colon
16	chr15:41258800-41268000	Weak transcription	Left Ventricle	heart
17	chr15:41258800-41268000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:41258800-41268200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:41258800-41268600	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:41258800-41268800	Weak transcription	Pancreas	Pancrea
21	chr15:41258800-41270400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:41258800-41270800	Weak transcription	Psoas Muscle	Psoas
23	chr15:41258800-41348400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr15:41259000-41268000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:41259000-41268000	Weak transcription	Liver	Liver
26	chr15:41259200-41268200	Weak transcription	NHLF	lung
27	chr15:41259400-41267800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:41259400-41268000	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:41259400-41268000	Weak transcription	HSMMtube	muscle
30	chr15:41259400-41268800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr15:41259600-41268000	Weak transcription	Fetal Kidney	kidney
32	chr15:41260800-41268200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:41260800-41268800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:41261200-41269400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:41261800-41268000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:41261800-41268000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:41261800-41268800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:41262000-41268000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:41262000-41271400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:41263800-41268000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr15:41263800-41268000	Weak transcription	Thymus	Thymus
42	chr15:41264000-41268000	Weak transcription	Small Intestine	intestine
43	chr15:41264000-41268200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr15:41264000-41275400	Weak transcription	Fetal Brain Male	brain
45	chr15:41264600-41267800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr15:41264600-41268000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:41264600-41268000	Weak transcription	Fetal Thymus	thymus
48	chr15:41264600-41268200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:41264600-41271800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr15:41264800-41267800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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