Variant report

Variant	rs28493702
Chromosome Location	chr15:41572702-41572703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10518717	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	1.00[ASN][1000 genomes]
rs11635269	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635565	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635906	1.00[ASN][1000 genomes]
rs11854081	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	1.00[ASN][1000 genomes]
rs11858068	1.00[ASN][1000 genomes]
rs11858812	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs13313520	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs13380007	0.94[YRI][hapmap]
rs16971726	1.00[CHB][hapmap];0.80[MEX][hapmap]
rs1757468	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs17730589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs2118740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs2730058	1.00[ASN][1000 genomes]
rs28374715	1.00[CHB][hapmap];0.87[MEX][hapmap]
rs28377562	0.86[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]
rs28437576	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448670	0.94[EUR][1000 genomes]
rs28456082	1.00[ASN][1000 genomes]
rs28458941	1.00[ASN][1000 genomes]
rs28463309	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28535540	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28554139	1.00[CHB][hapmap];0.80[MEX][hapmap];0.87[YRI][hapmap]
rs28555198	1.00[ASN][1000 genomes]
rs28557159	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs28576457	1.00[ASN][1000 genomes]
rs28584379	1.00[ASN][1000 genomes]
rs28617619	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28623183	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	1.00[ASN][1000 genomes]
rs28673484	1.00[ASN][1000 genomes]
rs28687846	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	1.00[ASN][1000 genomes]
rs28703570	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	0.93[AMR][1000 genomes];0.85[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	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs316607	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs316611	1.00[CHB][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs316616	1.00[ASN][1000 genomes]
rs3204853	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34040639	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs34665396	1.00[ASN][1000 genomes]
rs513280	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs521890	1.00[ASN][1000 genomes]
rs522063	1.00[CHB][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs55725658	1.00[ASN][1000 genomes]
rs56341337	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56400990	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493000	0.86[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	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163989	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164211	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs7164684	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs7165396	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165914	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168002	1.00[ASN][1000 genomes]
rs7168307	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168431	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs7169543	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	0.84[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	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	1.00[ASN][1000 genomes]
rs8023530	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs8030228	0.82[EUR][1000 genomes]
rs8034840	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	1.00[ASN][1000 genomes]
rs8037574	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038132	0.87[AMR][1000 genomes];0.91[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs28493702	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs28493702	NDUFAF1	cis	Thyroid	GTEx
rs28493702	NUSAP1	cis	parietal	SCAN
rs28493702	RASGRP1	cis	cerebellum	SCAN
rs28493702	NDUFAF1	cis	lymphoblastoid	seeQTL
rs28493702	OIP5-AS1	cis	Nerve Tibial	GTEx
rs28493702	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28493702	CASC5	cis	cerebellum	SCAN
rs28493702	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28493702	SPINT1	cis	cerebellum	SCAN
rs28493702	GPR176	cis	parietal	SCAN
rs28493702	NDUFAF1	cis	multi-tissue	Pritchard
rs28493702	OIP5-AS1	cis	Artery Tibial	GTEx
rs28493702	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs28493702	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28493702	NDUFAF1	cis	parietal	SCAN
rs28493702	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28493702	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28493702	NDUFAF1	cis	lung	GTEx
rs28493702	NUSAP1	cis	cerebellum	SCAN
rs28493702	PXDN	trans	lymphoblastoid	seeQTL
rs28493702	NDUFAF1	cis	cerebellum	SCAN
rs28493702	NDUFAF1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41524200-41575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:41525200-41575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:41525800-41575200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr15:41536600-41573600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:41543000-41575200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:41549200-41575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:41550400-41575600	Weak transcription	Fetal Brain Male	brain
8	chr15:41552400-41574600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:41552600-41575200	Weak transcription	GM12878-XiMat	blood
10	chr15:41552800-41575800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:41554600-41573000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:41556400-41574400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:41556800-41573200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:41556800-41575200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:41556800-41575200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:41556800-41575400	Weak transcription	Psoas Muscle	Psoas
17	chr15:41556800-41575800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:41556800-41575800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:41557000-41575400	Weak transcription	Fetal Heart	heart
20	chr15:41557200-41575200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:41557200-41575200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr15:41557800-41572800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:41559000-41575400	Weak transcription	Brain Germinal Matrix	brain
24	chr15:41561600-41572800	Strong transcription	Adipose Nuclei	Adipose
25	chr15:41562000-41573200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:41562000-41574000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:41563000-41575400	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:41564000-41575400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:41564000-41575400	Weak transcription	HUVEC	blood vessel
30	chr15:41564200-41575200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr15:41564200-41575400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:41564200-41576200	Weak transcription	Small Intestine	intestine
33	chr15:41568800-41573000	Strong transcription	Lung	lung
34	chr15:41569600-41573200	Weak transcription	NHDF-Ad	bronchial
35	chr15:41569600-41575400	Weak transcription	Fetal Brain Female	brain
36	chr15:41569600-41575400	Weak transcription	Stomach Mucosa	stomach
37	chr15:41569600-41575600	Weak transcription	Fetal Kidney	kidney
38	chr15:41570400-41572800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:41570600-41574000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:41570800-41573800	Enhancers	HepG2	liver
41	chr15:41571000-41572800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:41571000-41574800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr15:41571600-41572800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr15:41571800-41575200	Weak transcription	Fetal Intestine Small	intestine
45	chr15:41572000-41574000	Strong transcription	Liver	Liver
46	chr15:41572000-41574800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:41572000-41575200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:41572000-41575400	Weak transcription	Fetal Lung	lung
49	chr15:41572000-41576200	Weak transcription	Spleen	Spleen
50	chr15:41572200-41573400	Weak transcription	HSMM	muscle

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