Variant report

Variant	rs4244584
Chromosome Location	chr15:41259523-41259524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41229330..41231343-chr15:41257972..41259697,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1001341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1009913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11070314	0.86[EUR][1000 genomes]
rs11070315	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11070317	0.90[EUR][1000 genomes]
rs11855248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11856572	0.82[ASN][1000 genomes]
rs11856848	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs12593739	0.86[EUR][1000 genomes]
rs12899590	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12905926	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910027	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13329511	0.89[ASN][1000 genomes]
rs1678750	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs1869907	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1962410	0.81[ASN][1000 genomes]
rs2306083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs2412572	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412574	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28473405	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28479904	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28501589	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28538500	0.86[EUR][1000 genomes]
rs28572344	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28581803	0.84[ASN][1000 genomes]
rs2899002	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2925342	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2925343	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2925345	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2925346	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2927061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2927062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3100807	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3101436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3214068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3900905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3986311	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4497658	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs476633	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4923890	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924519	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924520	0.86[EUR][1000 genomes]
rs4924521	0.86[EUR][1000 genomes]
rs4924522	0.88[EUR][1000 genomes]
rs4924523	0.85[EUR][1000 genomes]
rs4924524	0.85[EUR][1000 genomes]
rs4924525	0.91[EUR][1000 genomes]
rs4924526	0.86[EUR][1000 genomes]
rs4924528	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924532	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60588038	0.86[EUR][1000 genomes]
rs692153	0.94[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs692155	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs7162992	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7171437	0.89[ASN][1000 genomes]
rs7174555	0.83[EUR][1000 genomes]
rs72735675	0.86[EUR][1000 genomes]
rs72737704	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8023345	0.81[ASN][1000 genomes]
rs8030306	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042088	0.82[ASN][1000 genomes]
rs8042127	0.83[EUR][1000 genomes]
rs9796	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv904106	chr15:41221067-41259523	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	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
rs4244584	NDUFAF1	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

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	chr15:41249400-41266000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:41249400-41268000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:41250000-41264400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:41252400-41269400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:41252800-41261000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:41252800-41270800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:41253600-41268200	Weak transcription	Spleen	Spleen
12	chr15:41253600-41268800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:41253600-41268800	Weak transcription	Right Ventricle	heart
14	chr15:41255800-41260800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:41257200-41259600	Enhancers	Fetal Stomach	stomach
16	chr15:41257800-41260000	Enhancers	Placenta	Placenta
17	chr15:41258200-41259600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr15:41258200-41259600	Enhancers	Fetal Lung	lung
19	chr15:41258400-41259600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr15:41258400-41261000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr15:41258600-41267600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:41258600-41268000	Weak transcription	Fetal Intestine Small	intestine
23	chr15:41258800-41260400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr15:41258800-41260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:41258800-41260800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:41258800-41260800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:41258800-41260800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:41258800-41261000	Weak transcription	Aorta	Aorta
29	chr15:41258800-41263600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:41258800-41264400	Weak transcription	K562	blood
31	chr15:41258800-41265200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:41258800-41266800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:41258800-41266800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:41258800-41267200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:41258800-41267800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:41258800-41267800	Weak transcription	Lung	lung
37	chr15:41258800-41267800	Weak transcription	Ovary	ovary
38	chr15:41258800-41268000	Weak transcription	Colonic Mucosa	Colon
39	chr15:41258800-41268000	Weak transcription	Left Ventricle	heart
40	chr15:41258800-41268000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr15:41258800-41268200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:41258800-41268600	Weak transcription	Brain Hippocampus Middle	brain
43	chr15:41258800-41268800	Weak transcription	Pancreas	Pancrea
44	chr15:41258800-41270400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr15:41258800-41270800	Weak transcription	Psoas Muscle	Psoas
46	chr15:41258800-41348400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr15:41259000-41260400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr15:41259000-41264200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:41259000-41268000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:41259000-41268000	Weak transcription	Liver	Liver

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