Variant report

Variant	rs28437576
Chromosome Location	chr15:41594303-41594304
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41593303..41595155-chr15:41597240..41599899,2	K562	blood:
2	chr15:41593982..41596712-chr15:41614556..41616645,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC012652.1.1-1	chr15:41590239-41598727	XLOC_011226
2	lnc-OIP5-1	chr15:41590239-41594387	XLOC_011448
3	lnc-AC012652.1.1-1	chr15:41590239-41598727	XLOC_011226
4	lnc-OIP5-1	chr15:41588773-41598741	XLOC_011448

No data

Extended variants
information (count: 109 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10518717	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132639	0.80[EUR][1000 genomes]
rs11629979	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630656	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	1.00[ASN][1000 genomes]
rs11635269	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635565	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635906	1.00[ASN][1000 genomes]
rs11854081	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	1.00[ASN][1000 genomes]
rs11858068	1.00[ASN][1000 genomes]
rs11858812	1.00[ASN][1000 genomes]
rs13313520	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs1757468	1.00[ASN][1000 genomes]
rs17730589	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	1.00[ASN][1000 genomes]
rs2730058	1.00[ASN][1000 genomes]
rs28377562	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	1.00[ASN][1000 genomes]
rs28421136	1.00[ASN][1000 genomes]
rs28448670	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28456082	1.00[ASN][1000 genomes]
rs28458941	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463309	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535540	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555198	1.00[ASN][1000 genomes]
rs28557159	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576457	1.00[ASN][1000 genomes]
rs28584379	1.00[ASN][1000 genomes]
rs28617619	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28623183	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	1.00[ASN][1000 genomes]
rs28673484	1.00[ASN][1000 genomes]
rs28687846	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	1.00[ASN][1000 genomes]
rs28703570	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	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	1.00[ASN][1000 genomes]
rs3204853	1.00[ASN][1000 genomes]
rs34665396	1.00[ASN][1000 genomes]
rs513280	1.00[ASN][1000 genomes]
rs521890	1.00[ASN][1000 genomes]
rs522063	1.00[ASN][1000 genomes]
rs55725658	1.00[ASN][1000 genomes]
rs56341337	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56400990	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493000	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493003	1.00[ASN][1000 genomes]
rs691011	1.00[ASN][1000 genomes]
rs691906	1.00[ASN][1000 genomes]
rs691907	1.00[ASN][1000 genomes]
rs7162231	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163989	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164211	1.00[ASN][1000 genomes]
rs7164684	1.00[ASN][1000 genomes]
rs7165396	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165914	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168002	1.00[ASN][1000 genomes]
rs7168307	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168431	1.00[ASN][1000 genomes]
rs7169543	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	0.89[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	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	1.00[ASN][1000 genomes]
rs8023530	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030228	0.88[EUR][1000 genomes]
rs8034840	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	1.00[ASN][1000 genomes]
rs8037574	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038132	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038983	1.00[ASN][1000 genomes]
rs8041809	1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs9568	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045455	chr15:41536624-41620534	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv984057	chr15:41590328-41596272	Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs28437576	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs28437576	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28437576	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28437576	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs28437576	NDUFAF1	cis	Thyroid	GTEx
rs28437576	OIP5-AS1	cis	Artery Tibial	GTEx
rs28437576	OIP5-AS1	cis	Nerve Tibial	GTEx
rs28437576	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28437576	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28437576	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28437576	NDUFAF1	cis	lung	GTEx
rs28437576	NDUFAF1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41577400-41610600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41577600-41606400	Weak transcription	Stomach Mucosa	stomach
3	chr15:41579200-41612400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:41580600-41603200	Weak transcription	Psoas Muscle	Psoas
5	chr15:41581200-41595200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:41581200-41596000	Weak transcription	Small Intestine	intestine
7	chr15:41581200-41598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:41581200-41601400	Weak transcription	NHDF-Ad	bronchial
9	chr15:41581200-41602200	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:41581200-41602600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:41581200-41604800	Weak transcription	Gastric	stomach
12	chr15:41581200-41605000	Weak transcription	Brain Substantia Nigra	brain
13	chr15:41581200-41607000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:41581200-41609600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr15:41581200-41623600	Weak transcription	Fetal Brain Male	brain
16	chr15:41581400-41605000	Weak transcription	HMEC	breast
17	chr15:41581400-41610400	Weak transcription	NHLF	lung
18	chr15:41581600-41601800	Weak transcription	Fetal Lung	lung
19	chr15:41581600-41623600	Weak transcription	Fetal Kidney	kidney
20	chr15:41583200-41623600	Weak transcription	HSMM	muscle
21	chr15:41583800-41613000	Weak transcription	Right Ventricle	heart
22	chr15:41584000-41604800	Weak transcription	Aorta	Aorta
23	chr15:41585000-41602800	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:41585600-41623600	Weak transcription	Primary B cells from cord blood	blood
25	chr15:41586200-41595000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr15:41586400-41595400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr15:41587200-41606800	Weak transcription	Fetal Heart	heart
28	chr15:41587600-41623000	Weak transcription	NHEK	skin
29	chr15:41588400-41600600	Weak transcription	Hela-S3	cervix
30	chr15:41589400-41601800	Weak transcription	K562	blood
31	chr15:41589400-41603600	Weak transcription	Spleen	Spleen
32	chr15:41589400-41604800	Weak transcription	Pancreas	Pancrea
33	chr15:41589600-41604800	Weak transcription	Lung	lung
34	chr15:41589600-41624000	Weak transcription	Esophagus	oesophagus
35	chr15:41590200-41601800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:41590200-41609200	Weak transcription	Colonic Mucosa	Colon
37	chr15:41590200-41623600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:41590400-41597000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:41590400-41600000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:41590600-41594800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:41590600-41601800	Weak transcription	Primary T cells from cord blood	blood
42	chr15:41590600-41602000	Weak transcription	Brain Germinal Matrix	brain
43	chr15:41590600-41603000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:41590600-41606800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:41590600-41623000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr15:41590800-41623000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr15:41591000-41606600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:41591200-41605000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:41591200-41623800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:41591200-41624000	Weak transcription	HSMMtube	muscle

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