Variant report

Variant	rs3986311
Chromosome Location	chr15:41264339-41264340
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41264244..41266968-chr15:41278240..41280821,2	MCF-7	breast:
2	chr15:41230059..41232086-chr15:41262058..41264861,2	MCF-7	breast:
3	chr15:41260659..41262903-chr15:41262940..41265797,2	K562	blood:
4	chr15:41251504..41254732-chr15:41263210..41265996,3	K562	blood:
5	chr15:41232946..41236246-chr15:41262141..41265286,3	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1001341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1009913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070314	0.87[EUR][1000 genomes]
rs11070315	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11070317	0.91[EUR][1000 genomes]
rs11854472	0.82[EUR][1000 genomes]
rs11855248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856572	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11856848	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12593739	0.87[EUR][1000 genomes]
rs12899590	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12905926	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910027	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13329511	0.90[ASN][1000 genomes]
rs1678750	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1869907	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869908	0.83[JPT][hapmap]
rs1962410	0.82[ASN][1000 genomes]
rs2306083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2412572	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412574	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28473405	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28479904	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28501589	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28538500	0.87[EUR][1000 genomes]
rs28572344	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28581803	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28613002	0.80[AFR][1000 genomes]
rs28688742	0.80[AFR][1000 genomes]
rs2899002	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2925342	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925343	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2925345	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2925346	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2927061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2927062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3100807	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3101436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3214068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3900905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4244584	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4497658	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476633	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4923890	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924519	0.87[EUR][1000 genomes]
rs4924520	0.87[EUR][1000 genomes]
rs4924521	0.87[EUR][1000 genomes]
rs4924522	0.86[EUR][1000 genomes]
rs4924523	0.86[EUR][1000 genomes]
rs4924524	0.86[EUR][1000 genomes]
rs4924525	0.89[EUR][1000 genomes]
rs4924526	0.87[EUR][1000 genomes]
rs4924528	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4924532	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60588038	0.87[EUR][1000 genomes]
rs6492978	0.80[ASN][1000 genomes]
rs692153	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs692155	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs7162992	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7169375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7171437	0.90[ASN][1000 genomes]
rs7174555	0.84[EUR][1000 genomes]
rs7179681	0.81[ASN][1000 genomes]
rs7181816	0.82[EUR][1000 genomes]
rs72735675	0.87[EUR][1000 genomes]
rs72737704	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8023345	0.81[ASN][1000 genomes]
rs8030306	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8042088	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8042127	0.84[EUR][1000 genomes]
rs9796	0.96[CEU][hapmap];0.85[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
rs3986311	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs3986311	NDUFAF1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:79 , 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	chr15:41252800-41270800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:41253600-41268200	Weak transcription	Spleen	Spleen
11	chr15:41253600-41268800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:41253600-41268800	Weak transcription	Right Ventricle	heart
13	chr15:41258600-41267600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:41258600-41268000	Weak transcription	Fetal Intestine Small	intestine
15	chr15:41258800-41264400	Weak transcription	K562	blood
16	chr15:41258800-41265200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:41258800-41266800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr15:41258800-41266800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:41258800-41267200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:41258800-41267800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:41258800-41267800	Weak transcription	Lung	lung
22	chr15:41258800-41267800	Weak transcription	Ovary	ovary
23	chr15:41258800-41268000	Weak transcription	Colonic Mucosa	Colon
24	chr15:41258800-41268000	Weak transcription	Left Ventricle	heart
25	chr15:41258800-41268000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr15:41258800-41268200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:41258800-41268600	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:41258800-41268800	Weak transcription	Pancreas	Pancrea
29	chr15:41258800-41270400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:41258800-41270800	Weak transcription	Psoas Muscle	Psoas
31	chr15:41258800-41348400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr15:41259000-41268000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:41259000-41268000	Weak transcription	Liver	Liver
34	chr15:41259200-41266800	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:41259200-41268200	Weak transcription	NHLF	lung
36	chr15:41259400-41266600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:41259400-41267000	Weak transcription	Brain Germinal Matrix	brain
38	chr15:41259400-41267800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:41259400-41268000	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:41259400-41268000	Weak transcription	HSMMtube	muscle
41	chr15:41259400-41268800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:41259600-41264600	Weak transcription	Fetal Lung	lung
43	chr15:41259600-41268000	Weak transcription	Fetal Kidney	kidney
44	chr15:41260000-41266800	Weak transcription	Placenta	Placenta
45	chr15:41260800-41264400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:41260800-41268200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:41260800-41268800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:41261000-41264400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:41261000-41267000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:41261200-41269400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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