Variant report

Variant	rs11854820
Chromosome Location	chr15:41676526-41676527
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	chr15:41672888..41674609-chr15:41676088..41678675,2	K562	blood:

Extended variants
information (count: 113 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10518717	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	1.00[ASN][1000 genomes]
rs11630656	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11635906	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854081	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs1757468	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730589	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377562	1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28421136	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	1.00[ASN][1000 genomes]
rs28448670	0.89[AMR][1000 genomes]
rs28456082	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458941	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459164	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28463309	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	1.00[ASN][1000 genomes]
rs28535540	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555198	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	1.00[ASN][1000 genomes]
rs28576457	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584379	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673484	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703570	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316606	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316607	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316611	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316616	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204853	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34040639	0.86[EUR][1000 genomes]
rs34285452	0.90[EUR][1000 genomes]
rs34665396	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513280	1.00[ASN][1000 genomes]
rs521890	1.00[ASN][1000 genomes]
rs522063	1.00[ASN][1000 genomes]
rs55725658	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56341337	0.81[EUR][1000 genomes]
rs56400990	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	1.00[ASN][1000 genomes]
rs6493000	1.00[ASN][1000 genomes]
rs6493003	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691011	1.00[ASN][1000 genomes]
rs691906	1.00[ASN][1000 genomes]
rs691907	1.00[ASN][1000 genomes]
rs7162231	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7164211	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164684	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	1.00[ASN][1000 genomes]
rs7165914	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	1.00[ASN][1000 genomes]
rs7168431	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	1.00[ASN][1000 genomes]
rs72737786	1.00[ASN][1000 genomes]
rs72737792	1.00[ASN][1000 genomes]
rs72737793	1.00[ASN][1000 genomes]
rs72739630	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	1.00[ASN][1000 genomes]
rs8034840	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	1.00[ASN][1000 genomes]
rs8038132	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8038983	1.00[ASN][1000 genomes]
rs8041809	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs9568	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
5	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
6	esv3443258	chr15:41644871-41681515	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3409890	chr15:41644895-41681538	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3407946	chr15:41674085-41676633	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11854820	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs11854820	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs11854820	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs11854820	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs11854820	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs11854820	NDUFAF1	cis	Muscle Skeletal	GTEx
rs11854820	NDUFAF1	cis	multi-tissue	Pritchard
rs11854820	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs11854820	NDUFAF1	cis	lung	GTEx
rs11854820	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs11854820	OIP5-AS1	cis	Nerve Tibial	GTEx
rs11854820	OIP5-AS1	cis	Artery Tibial	GTEx
rs11854820	NDUFAF1	cis	Thyroid	GTEx
rs11854820	NDUFAF1	cis	Whole Blood	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41625800-41694200	Weak transcription	Small Intestine	intestine
2	chr15:41626200-41678200	Weak transcription	Liver	Liver
3	chr15:41626200-41680200	Weak transcription	Fetal Brain Male	brain
4	chr15:41626400-41677800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:41626400-41678400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:41626800-41686400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:41627200-41676800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:41631800-41679200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:41642800-41679400	Weak transcription	Ovary	ovary
10	chr15:41643800-41679000	Weak transcription	Pancreas	Pancrea
11	chr15:41644200-41678600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr15:41644200-41679800	Weak transcription	Primary B cells from cord blood	blood
13	chr15:41654200-41678200	Weak transcription	HSMMtube	muscle
14	chr15:41659400-41677800	Weak transcription	Lung	lung
15	chr15:41659600-41678800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr15:41659800-41680000	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:41660000-41678200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr15:41660200-41677800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:41660200-41688400	Weak transcription	Esophagus	oesophagus
20	chr15:41660200-41693800	Weak transcription	Right Ventricle	heart
21	chr15:41660600-41679600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:41660600-41680000	Weak transcription	Psoas Muscle	Psoas
23	chr15:41661400-41679600	Weak transcription	Fetal Kidney	kidney
24	chr15:41661800-41693200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:41663400-41677800	Weak transcription	Adipose Nuclei	Adipose
26	chr15:41664600-41679800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:41664800-41678200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:41665200-41688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:41665800-41683400	Weak transcription	Left Ventricle	heart
30	chr15:41666400-41686400	Weak transcription	Brain Anterior Caudate	brain
31	chr15:41666600-41680000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:41667000-41678200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:41668400-41678200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:41669000-41687000	Weak transcription	Aorta	Aorta
35	chr15:41669600-41678600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:41669600-41684400	Weak transcription	Brain Substantia Nigra	brain
37	chr15:41670600-41678400	Weak transcription	NHLF	lung
38	chr15:41670600-41679600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:41670600-41686400	Weak transcription	NH-A	brain
40	chr15:41670800-41678400	Weak transcription	Placenta	Placenta
41	chr15:41670800-41678600	Weak transcription	Fetal Brain Female	brain
42	chr15:41670800-41686400	Weak transcription	Gastric	stomach
43	chr15:41671000-41677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:41671600-41678800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:41672000-41693600	Weak transcription	Colonic Mucosa	Colon
46	chr15:41672200-41677600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:41672200-41679000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:41672600-41678200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:41672600-41678600	Weak transcription	Fetal Intestine Large	intestine
50	chr15:41673000-41677800	Weak transcription	Thymus	Thymus

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