Variant report

Variant	rs28897479
Chromosome Location	chr15:41690851-41690852
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10518717	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070328	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	1.00[ASN][1000 genomes]
rs11630656	1.00[ASN][1000 genomes]
rs11630799	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11635906	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854081	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs1757468	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730589	1.00[ASN][1000 genomes]
rs17730888	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377562	1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28421136	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	1.00[ASN][1000 genomes]
rs28448670	0.86[AMR][1000 genomes]
rs28456082	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458941	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459164	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28463309	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	1.00[ASN][1000 genomes]
rs28535540	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555198	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	1.00[ASN][1000 genomes]
rs28576457	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584379	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673484	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	1.00[ASN][1000 genomes]
rs28700583	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703570	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs316604	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316606	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316607	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316611	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316616	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34040639	0.87[EUR][1000 genomes]
rs34285452	0.91[EUR][1000 genomes]
rs34665396	0.98[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	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56341337	0.82[EUR][1000 genomes]
rs56400990	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	1.00[ASN][1000 genomes]
rs6493000	1.00[ASN][1000 genomes]
rs6493003	0.97[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	1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7164211	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164684	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	1.00[ASN][1000 genomes]
rs7165914	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	1.00[ASN][1000 genomes]
rs7168431	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	1.00[ASN][1000 genomes]
rs7181982	0.80[EUR][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	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	1.00[ASN][1000 genomes]
rs8034840	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	1.00[ASN][1000 genomes]
rs8038132	1.00[ASN][1000 genomes]
rs8038983	1.00[ASN][1000 genomes]
rs8041809	0.97[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:6 , 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	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs28897479	NDUFAF1	cis	Whole Blood	GTEx
rs28897479	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28897479	NDUFAF1	cis	multi-tissue	Pritchard
rs28897479	NDUFAF1	cis	Thyroid	GTEx
rs28897479	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28897479	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28897479	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs28897479	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs28897479	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28897479	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs28897479	OIP5-AS1	cis	Nerve Tibial	GTEx
rs28897479	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28897479	OIP5-AS1	cis	Artery Tibial	GTEx
rs28897479	NDUFAF1	cis	lung	GTEx

Chromatin state (count:124 , 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	chr15:41660200-41693800	Weak transcription	Right Ventricle	heart
3	chr15:41661800-41693200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:41672000-41693600	Weak transcription	Colonic Mucosa	Colon
5	chr15:41673400-41693800	Weak transcription	HMEC	breast
6	chr15:41673600-41693800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:41673600-41693800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:41673800-41693600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr15:41674000-41693800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:41674000-41693800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:41676400-41692200	Strong transcription	Fetal Stomach	stomach
12	chr15:41677000-41693400	Weak transcription	HepG2	liver
13	chr15:41677200-41693400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:41678400-41693800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:41679200-41693800	Weak transcription	Stomach Mucosa	stomach
16	chr15:41680000-41691400	Strong transcription	Fetal Muscle Leg	muscle
17	chr15:41680000-41694000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:41681200-41693800	Weak transcription	NHDF-Ad	bronchial
19	chr15:41682000-41693200	Weak transcription	Psoas Muscle	Psoas
20	chr15:41685400-41691600	Strong transcription	Fetal Intestine Small	intestine
21	chr15:41685400-41693800	Weak transcription	Fetal Heart	heart
22	chr15:41687400-41693600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:41687400-41693800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:41687400-41693800	Weak transcription	A549	lung
25	chr15:41687400-41694000	Weak transcription	Fetal Kidney	kidney
26	chr15:41687600-41693800	Weak transcription	K562	blood
27	chr15:41688800-41693600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:41688800-41693800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:41688800-41693800	Weak transcription	Brain Germinal Matrix	brain
30	chr15:41688800-41693800	Weak transcription	Gastric	stomach
31	chr15:41688800-41693800	Weak transcription	NHEK	skin
32	chr15:41689000-41693400	Weak transcription	Primary B cells from cord blood	blood
33	chr15:41689000-41693400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:41689000-41693400	Weak transcription	Thymus	Thymus
35	chr15:41689000-41693600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:41689000-41693600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:41689000-41693600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:41689000-41693600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr15:41689000-41693600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:41689000-41693600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr15:41689000-41693600	Weak transcription	Brain Substantia Nigra	brain
42	chr15:41689000-41693600	Weak transcription	Esophagus	oesophagus
43	chr15:41689000-41693600	Weak transcription	Fetal Brain Male	brain
44	chr15:41689000-41693600	Weak transcription	Fetal Lung	lung
45	chr15:41689000-41693800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:41689000-41693800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:41689000-41693800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:41689000-41693800	Weak transcription	HUVEC	blood vessel
49	chr15:41689000-41693800	Weak transcription	NHLF	lung
50	chr15:41689000-41694000	Weak transcription	Aorta	Aorta

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