Variant report

Variant	rs544744
Chromosome Location	chr15:41366290-41366291
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1009913	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11853192	0.99[ASN][1000 genomes]
rs11854472	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11855797	0.85[ASN][1000 genomes]
rs11856572	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11856577	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856848	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12101934	0.86[ASN][1000 genomes]
rs12905926	0.82[EUR][1000 genomes]
rs12910027	0.82[EUR][1000 genomes]
rs1678750	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1717200	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1962410	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1983400	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2176998	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306083	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412601	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28409432	0.86[ASN][1000 genomes]
rs28455998	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28510775	1.00[ASN][1000 genomes]
rs28516683	0.86[ASN][1000 genomes]
rs28581803	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28613002	0.95[ASN][1000 genomes]
rs28688742	0.95[ASN][1000 genomes]
rs28729675	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28866311	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2925342	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2925345	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2925346	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2927061	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2927062	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2928148	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2928156	0.86[ASN][1000 genomes]
rs2947493	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2947494	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3100807	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3101436	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3101442	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3214068	0.83[EUR][1000 genomes]
rs36046988	0.84[ASN][1000 genomes]
rs4592624	0.97[ASN][1000 genomes]
rs476633	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs516156	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs561301	0.86[ASN][1000 genomes]
rs57393155	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61203391	0.86[ASN][1000 genomes]
rs6492982	0.87[AFR][1000 genomes]
rs6492983	0.86[ASN][1000 genomes]
rs66818965	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs691672	0.85[ASN][1000 genomes]
rs691830	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs692153	0.86[ASN][1000 genomes]
rs692155	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs692195	0.86[ASN][1000 genomes]
rs7162992	0.82[EUR][1000 genomes]
rs7169375	0.82[EUR][1000 genomes]
rs7173841	0.86[ASN][1000 genomes]
rs7179681	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7180853	0.86[ASN][1000 genomes]
rs7181816	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72737704	0.86[EUR][1000 genomes]
rs8023345	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8027932	0.85[ASN][1000 genomes]
rs8033435	0.86[ASN][1000 genomes]
rs8037837	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8042088	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9888710	0.86[ASN][1000 genomes]
rs9888718	0.86[ASN][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	nsv1053462	chr15:41270067-41396094	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv974711	chr15:41360002-41370961	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs544744	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs544744	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs544744	OIP5-AS1	cis	Artery Tibial	GTEx
rs544744	NDUFAF1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41328800-41388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:41334600-41389000	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr15:41336800-41380400	Strong transcription	Osteobl	bone
4	chr15:41340800-41366800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:41341600-41389000	Strong transcription	Liver	Liver
6	chr15:41345200-41373600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:41346800-41368600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:41347000-41380200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:41354000-41368600	Strong transcription	NH-A	brain
10	chr15:41354200-41389200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:41354600-41367400	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr15:41354600-41388800	Strong transcription	Fetal Intestine Large	intestine
13	chr15:41354600-41389000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr15:41354800-41388600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr15:41354800-41389200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:41355000-41367200	Strong transcription	Ovary	ovary
17	chr15:41355000-41367400	Strong transcription	Adipose Nuclei	Adipose
18	chr15:41355000-41369200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:41355000-41370800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr15:41355000-41374200	Strong transcription	Hela-S3	cervix
21	chr15:41355000-41380200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:41355000-41380800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:41355000-41381000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:41355000-41388400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:41355000-41389400	Strong transcription	Placenta	Placenta
26	chr15:41355000-41392000	Strong transcription	Fetal Thymus	thymus
27	chr15:41355000-41392400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:41355000-41393800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:41355200-41367200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:41355200-41370600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:41355200-41388600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:41355200-41388800	Strong transcription	Primary T cells from cord blood	blood
33	chr15:41355400-41368800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:41355400-41369000	Strong transcription	Thymus	Thymus
35	chr15:41355400-41369200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:41355400-41370800	Weak transcription	Pancreas	Pancrea
37	chr15:41355400-41371800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:41355400-41378400	Strong transcription	Fetal Muscle Leg	muscle
39	chr15:41355400-41383200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:41355400-41388800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:41355400-41389200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:41355400-41390200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:41355400-41393200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:41355600-41370800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:41355600-41390800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr15:41355800-41367200	Strong transcription	NHEK	skin
47	chr15:41355800-41370800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:41355800-41381800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:41355800-41389200	Strong transcription	Dnd41	blood
50	chr15:41355800-41391000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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