Variant report

Variant	rs10518717
Chromosome Location	chr15:41623368-41623369
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41523451..41525633-chr15:41623235..41625068,3	K562	blood:
2	chr15:41621801..41625398-chr15:41692470..41696241,5	K562	blood:
3	chr15:41407574..41409310-chr15:41622908..41625714,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187446	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000137806	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630656	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	1.00[ASN][1000 genomes]
rs11635269	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635565	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11854081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs16971726	1.00[CHB][hapmap]
rs1757468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17730589	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	1.00[ASN][1000 genomes]
rs28374715	1.00[CHB][hapmap]
rs28377562	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	1.00[ASN][1000 genomes]
rs28421136	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448670	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28456082	1.00[ASN][1000 genomes]
rs28458941	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535540	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28554139	1.00[CHB][hapmap]
rs28555198	1.00[ASN][1000 genomes]
rs28557159	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576457	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584379	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28623183	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28631111	1.00[CHB][hapmap]
rs28661013	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673484	1.00[ASN][1000 genomes]
rs28687846	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	1.00[ASN][1000 genomes]
rs28703570	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs316606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs316607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs316611	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs316616	1.00[ASN][1000 genomes]
rs3204853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34040639	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs34665396	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924549	1.00[CHB][hapmap]
rs513280	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs521890	1.00[ASN][1000 genomes]
rs522063	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55725658	1.00[ASN][1000 genomes]
rs56341337	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56400990	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493000	0.88[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	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163989	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168002	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[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	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	1.00[ASN][1000 genomes]
rs8023530	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030228	0.88[EUR][1000 genomes]
rs8034840	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038132	0.87[AMR][1000 genomes];0.97[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	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[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	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	nsv977843	chr15:41608625-41625613	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	44 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs10518717	NDUFAF1	cis	Muscle Skeletal	GTEx
rs10518717	NDUFAF1	cis	lung	GTEx
rs10518717	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs10518717	NDUFAF1	cis	multi-tissue	Pritchard
rs10518717	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs10518717	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs10518717	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs10518717	NDUFAF1	cis	Thyroid	GTEx
rs10518717	OIP5-AS1	cis	Nerve Tibial	GTEx
rs10518717	KRTAP4-7	cis	lesional skin	skin_eQTL
rs10518717	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs10518717	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs10518717	OIP5-AS1	cis	Artery Tibial	GTEx
rs10518717	KRTAP4-7	cis	normal skin	skin_eQTL
rs10518717	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs10518717	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41581200-41623600	Weak transcription	Fetal Brain Male	brain
2	chr15:41581600-41623600	Weak transcription	Fetal Kidney	kidney
3	chr15:41583200-41623600	Weak transcription	HSMM	muscle
4	chr15:41585600-41623600	Weak transcription	Primary B cells from cord blood	blood
5	chr15:41589600-41624000	Weak transcription	Esophagus	oesophagus
6	chr15:41590200-41623600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:41591200-41623800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:41591200-41624000	Weak transcription	HSMMtube	muscle
9	chr15:41591800-41624000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:41592400-41624000	Weak transcription	Brain Angular Gyrus	brain
11	chr15:41592600-41623800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr15:41593600-41623800	Weak transcription	NH-A	brain
13	chr15:41600600-41623600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:41602400-41623600	Weak transcription	NHDF-Ad	bronchial
15	chr15:41603400-41623400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:41603800-41623600	Weak transcription	Fetal Lung	lung
17	chr15:41604200-41624000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:41605800-41623400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr15:41605800-41623800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:41605800-41623800	Weak transcription	Adipose Nuclei	Adipose
21	chr15:41606400-41623600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr15:41608200-41624200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:41608800-41623600	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:41610000-41624000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr15:41610800-41623400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:41610800-41623600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:41611800-41623600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:41612000-41623400	Weak transcription	Thymus	Thymus
29	chr15:41612000-41623600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr15:41612000-41623600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:41616600-41623600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr15:41616600-41624000	Weak transcription	Brain Substantia Nigra	brain
33	chr15:41617800-41623400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:41618800-41623600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:41619000-41623600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:41619000-41623600	Weak transcription	Fetal Brain Female	brain
37	chr15:41619200-41623400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:41619200-41623800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:41620600-41623600	Weak transcription	Fetal Stomach	stomach
40	chr15:41621000-41623400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:41622400-41624000	Enhancers	Colonic Mucosa	Colon
42	chr15:41622600-41623600	Weak transcription	Primary T cells from cord blood	blood
43	chr15:41622800-41623400	Enhancers	HepG2	liver
44	chr15:41623000-41623400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr15:41623000-41623400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:41623000-41623400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr15:41623000-41623400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:41623000-41623400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:41623000-41623400	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr15:41623000-41623400	Enhancers	Fetal Thymus	thymus

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