Variant report

Variant	rs2099652
Chromosome Location	chr15:41528745-41528746
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13329240	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16952331	0.91[ASN][1000 genomes]
rs16971647	0.89[ASN][1000 genomes]
rs16971651	0.89[ASN][1000 genomes]
rs16971653	0.89[ASN][1000 genomes]
rs16971654	0.89[ASN][1000 genomes]
rs16971733	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16971735	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2083238	0.95[ASN][1000 genomes]
rs2090826	0.89[ASN][1000 genomes]
rs2412607	0.89[ASN][1000 genomes]
rs28417774	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28468975	0.91[AMR][1000 genomes]
rs28478807	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28626792	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55787465	0.89[ASN][1000 genomes]
rs55952963	0.89[ASN][1000 genomes]
rs56262456	0.89[ASN][1000 genomes]
rs57009745	0.89[ASN][1000 genomes]
rs57896923	0.87[ASN][1000 genomes]
rs58060180	0.91[ASN][1000 genomes]
rs58436082	0.91[ASN][1000 genomes]
rs58851405	0.89[ASN][1000 genomes]
rs6492995	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492996	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165551	0.89[ASN][1000 genomes]
rs7166182	0.88[ASN][1000 genomes]
rs7166581	0.84[ASN][1000 genomes]
rs7167142	0.86[ASN][1000 genomes]
rs8025660	0.83[ASN][1000 genomes]
rs8025916	0.89[ASN][1000 genomes]
rs8029873	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8030033	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8030683	0.89[ASN][1000 genomes]
rs8030706	0.89[ASN][1000 genomes]
rs8030712	0.89[ASN][1000 genomes]
rs8030732	0.89[ASN][1000 genomes]
rs8030954	0.89[ASN][1000 genomes]
rs8034073	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8034924	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8036686	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457120	chr15:41410705-41546631	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv569231	chr15:41410705-41546631	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv1844058	chr15:41511916-41548948	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2099652	NDUFAF1	cis	multi-tissue	Pritchard
rs2099652	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs2099652	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs2099652	OIP5-AS1	cis	Artery Tibial	GTEx
rs2099652	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs2099652	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs2099652	NDUFAF1	cis	Muscle Skeletal	GTEx
rs2099652	NDUFAF1	cis	Thyroid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41524200-41533200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:41524200-41533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41524200-41535800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:41524200-41536600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:41524200-41546200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:41524200-41554800	Weak transcription	Fetal Thymus	thymus
7	chr15:41524200-41555800	Weak transcription	Aorta	Aorta
8	chr15:41524200-41563800	Weak transcription	Small Intestine	intestine
9	chr15:41524200-41575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:41524400-41532400	Weak transcription	Fetal Intestine Small	intestine
11	chr15:41524400-41533400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:41524400-41533600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:41524400-41533600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:41524400-41535800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:41524400-41536600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:41524400-41555800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:41524600-41533400	Weak transcription	Primary B cells from cord blood	blood
18	chr15:41524600-41533600	Weak transcription	Thymus	Thymus
19	chr15:41524600-41536400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:41524600-41536600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:41524800-41533000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr15:41524800-41533200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:41524800-41533400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:41524800-41533600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:41524800-41535800	Weak transcription	Ovary	ovary
26	chr15:41524800-41546200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr15:41524800-41563800	Weak transcription	Esophagus	oesophagus
28	chr15:41525000-41530600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:41525000-41533400	Weak transcription	Primary T cells from cord blood	blood
30	chr15:41525000-41533600	Weak transcription	Placenta	Placenta
31	chr15:41525000-41535400	Weak transcription	Fetal Stomach	stomach
32	chr15:41525000-41548400	Weak transcription	Fetal Lung	lung
33	chr15:41525200-41532600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:41525200-41533400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:41525200-41533400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:41525200-41533400	Weak transcription	Brain Anterior Caudate	brain
37	chr15:41525200-41533600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:41525200-41533600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:41525200-41548200	Weak transcription	Fetal Kidney	kidney
40	chr15:41525200-41554200	Weak transcription	Fetal Brain Female	brain
41	chr15:41525200-41556400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:41525200-41575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr15:41525400-41529600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:41525400-41530200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:41525400-41532400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:41525400-41532400	Weak transcription	Fetal Intestine Large	intestine
47	chr15:41525400-41533200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr15:41525400-41533400	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:41525400-41533400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:41525400-41533600	Weak transcription	Primary B cells from peripheral blood	blood

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