Variant report

Variant	rs56400990
Chromosome Location	chr15:41654864-41654865
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	chr15:41653827..41656033-chr15:41656188..41659095,2	K562	blood:

Variant related genes	Relation type
ENSG00000137804	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10518717	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630656	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635269	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635565	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635906	1.00[ASN][1000 genomes]
rs11854081	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs1757468	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730589	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377562	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28421136	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448670	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28456082	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458941	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459164	0.84[EUR][1000 genomes]
rs28463309	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535540	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555198	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576457	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584379	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28623183	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673484	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703570	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	1.00[ASN][1000 genomes]
rs316606	1.00[ASN][1000 genomes]
rs316607	1.00[ASN][1000 genomes]
rs316611	1.00[ASN][1000 genomes]
rs316616	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204853	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34665396	0.82[AMR][1000 genomes];0.86[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	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56341337	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59000092	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493000	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493003	0.85[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	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7164211	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164684	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165914	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168002	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168431	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737786	1.00[ASN][1000 genomes]
rs72737792	1.00[ASN][1000 genomes]
rs72737793	1.00[ASN][1000 genomes]
rs72739630	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030228	0.84[EUR][1000 genomes]
rs8034840	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038132	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038983	1.00[ASN][1000 genomes]
rs8041809	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs9568	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs56400990	NDUFAF1	cis	Thyroid	GTEx
rs56400990	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs56400990	NDUFAF1	cis	lung	GTEx
rs56400990	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs56400990	NDUFAF1	cis	Muscle Skeletal	GTEx
rs56400990	OIP5-AS1	cis	Artery Tibial	GTEx
rs56400990	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs56400990	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs56400990	OIP5-AS1	cis	Nerve Tibial	GTEx
rs56400990	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs56400990	NDUFAF1	cis	Whole Blood	GTEx
rs56400990	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs56400990	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41625400-41670200	Weak transcription	Gastric	stomach
2	chr15:41625600-41659200	Weak transcription	Lung	lung
3	chr15:41625800-41665800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:41625800-41694200	Weak transcription	Small Intestine	intestine
5	chr15:41626000-41665200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:41626200-41658200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:41626200-41678200	Weak transcription	Liver	Liver
8	chr15:41626200-41680200	Weak transcription	Fetal Brain Male	brain
9	chr15:41626400-41677800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:41626400-41678400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:41626800-41686400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:41627000-41672800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:41627200-41676800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:41627400-41668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:41627400-41673000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:41628200-41673000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:41628600-41672800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:41628600-41673800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:41629000-41672000	Weak transcription	Primary T cells from cord blood	blood
20	chr15:41629000-41673000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:41629400-41672400	Strong transcription	Fetal Stomach	stomach
22	chr15:41629400-41672800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:41629400-41673600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:41629600-41674000	Strong transcription	Fetal Thymus	thymus
25	chr15:41629800-41658800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:41630000-41662000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:41630400-41674000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:41630400-41674200	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr15:41630800-41673800	Strong transcription	Dnd41	blood
30	chr15:41631200-41659200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr15:41631800-41679200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:41632000-41673000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:41632000-41673600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:41632200-41655000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:41632200-41659600	Strong transcription	Fetal Muscle Leg	muscle
36	chr15:41632200-41674000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:41632800-41673800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:41638400-41658800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:41639200-41671800	Strong transcription	Hela-S3	cervix
40	chr15:41639800-41657400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:41640800-41674000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:41642800-41679400	Weak transcription	Ovary	ovary
43	chr15:41643600-41658800	Weak transcription	Fetal Brain Female	brain
44	chr15:41643800-41658800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr15:41643800-41659000	Weak transcription	Fetal Heart	heart
46	chr15:41643800-41679000	Weak transcription	Pancreas	Pancrea
47	chr15:41644000-41657000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:41644000-41658600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:41644000-41659200	Weak transcription	Spleen	Spleen
50	chr15:41644000-41670200	Weak transcription	Placenta	Placenta

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