Variant report

Variant	rs7176588
Chromosome Location	chr15:41588872-41588873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41581933..41584889-chr15:41587370..41590303,3	K562	blood:
2	chr15:41587115..41589389-chr15:41693080..41695951,2	MCF-7	breast:
3	chr15:41574707..41576422-chr15:41588178..41590438,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OIP5-1	chr15:41588773-41598741	XLOC_011448

Variant related genes	Relation type
ENSG00000247556	Chromatin interaction
ENSG00000137806	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10152497	0.88[ASN][1000 genomes]
rs10152702	0.81[ASN][1000 genomes]
rs10153010	0.88[ASN][1000 genomes]
rs10467974	0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10518718	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11549913	0.87[ASN][1000 genomes]
rs11630191	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11631770	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[ASN][1000 genomes]
rs11633799	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852609	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11857631	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12324291	0.91[ASN][1000 genomes]
rs13379756	0.82[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs16971767	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16971798	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16971806	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16971832	0.91[JPT][hapmap]
rs16971834	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs1757463	0.81[CHB][hapmap]
rs2015781	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2777491	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs28393472	0.88[ASN][1000 genomes]
rs28526381	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28557159	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs28578057	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28583065	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28600680	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28643296	0.95[ASN][1000 genomes]
rs28655070	0.81[ASN][1000 genomes]
rs28716108	0.93[ASN][1000 genomes]
rs28792672	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs316605	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs316609	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs316610	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs316613	0.82[ASN][1000 genomes]
rs316614	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs35826725	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3743038	0.95[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55782852	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58335029	0.91[ASN][1000 genomes]
rs58910172	0.95[ASN][1000 genomes]
rs59590312	0.90[ASN][1000 genomes]
rs61037359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61127691	0.95[ASN][1000 genomes]
rs6650519	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66538814	0.92[ASN][1000 genomes]
rs7161772	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7163649	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163788	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7165675	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167498	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7167729	0.87[ASN][1000 genomes]
rs7168177	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7168307	0.82[GIH][hapmap];0.84[MEX][hapmap]
rs7172148	0.82[ASN][1000 genomes]
rs7175690	0.95[ASN][1000 genomes]
rs7175800	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7176314	0.95[ASN][1000 genomes]
rs7176505	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7177641	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs7178634	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7178777	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs7180418	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7181560	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7181911	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7182667	0.91[ASN][1000 genomes]
rs7182700	0.82[ASN][1000 genomes]
rs7183337	0.91[ASN][1000 genomes]
rs73404980	0.88[ASN][1000 genomes]
rs73404987	0.93[ASN][1000 genomes]
rs73404994	0.88[ASN][1000 genomes]
rs73404995	0.88[ASN][1000 genomes]
rs73404996	0.88[ASN][1000 genomes]
rs73405000	0.86[ASN][1000 genomes]
rs73405001	0.86[ASN][1000 genomes]
rs73407109	0.88[ASN][1000 genomes]
rs8023530	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs8023619	0.93[ASN][1000 genomes]
rs8026197	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8027626	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8032838	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034626	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8034819	0.82[ASN][1000 genomes]
rs8036498	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8037574	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs8037824	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8041325	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs823716	0.95[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs919961	0.88[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9302109	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9672866	0.84[ASN][1000 genomes]
rs9972288	0.89[ASN][1000 genomes]
rs9972547	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs7176588	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs7176588	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs7176588	NDUFAF1	cis	multi-tissue	Pritchard
rs7176588	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs7176588	NUSAP1	cis	cerebellum	SCAN
rs7176588	NDUFAF1	cis	parietal	SCAN
rs7176588	OIP5-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs7176588	NUSAP1	cis	parietal	SCAN
rs7176588	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs7176588	NDUFAF1	cis	Muscle Skeletal	GTEx
rs7176588	NDUFAF1	cis	Thyroid	GTEx
rs7176588	OIP5-AS1	cis	Artery Tibial	GTEx
rs7176588	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs7176588	NDUFAF1	cis	lymphoblastoid	seeQTL
rs7176588	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs7176588	CASC5	cis	cerebellum	SCAN
rs7176588	RPAP1	cis	parietal	SCAN
rs7176588	OIP5-AS1	cis	Nerve Tibial	GTEx
rs7176588	NDUFAF1	cis	cerebellum	SCAN
rs7176588	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs7176588	OIP5-AS1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 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	chr15:41577800-41589000	Weak transcription	Esophagus	oesophagus
4	chr15:41577800-41591600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:41578000-41591600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:41578200-41591800	Strong transcription	Fetal Stomach	stomach
7	chr15:41578200-41592600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:41578400-41592600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:41578800-41591800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:41579200-41593200	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:41579200-41612400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:41580000-41592600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:41580600-41603200	Weak transcription	Psoas Muscle	Psoas
14	chr15:41581000-41590000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:41581000-41593200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:41581200-41589000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:41581200-41589000	Weak transcription	Ovary	ovary
18	chr15:41581200-41589000	Weak transcription	Spleen	Spleen
19	chr15:41581200-41589000	Weak transcription	HSMMtube	muscle
20	chr15:41581200-41589200	Weak transcription	Colonic Mucosa	Colon
21	chr15:41581200-41589200	Weak transcription	Pancreas	Pancrea
22	chr15:41581200-41592200	Weak transcription	Brain Angular Gyrus	brain
23	chr15:41581200-41592200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:41581200-41592400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:41581200-41593000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:41581200-41595200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:41581200-41596000	Weak transcription	Small Intestine	intestine
28	chr15:41581200-41598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:41581200-41601400	Weak transcription	NHDF-Ad	bronchial
30	chr15:41581200-41602200	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:41581200-41602600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr15:41581200-41604800	Weak transcription	Gastric	stomach
33	chr15:41581200-41605000	Weak transcription	Brain Substantia Nigra	brain
34	chr15:41581200-41607000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr15:41581200-41609600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:41581200-41623600	Weak transcription	Fetal Brain Male	brain
37	chr15:41581400-41589200	Weak transcription	HUVEC	blood vessel
38	chr15:41581400-41605000	Weak transcription	HMEC	breast
39	chr15:41581400-41610400	Weak transcription	NHLF	lung
40	chr15:41581600-41589000	Weak transcription	Brain Anterior Caudate	brain
41	chr15:41581600-41589200	Weak transcription	Placenta	Placenta
42	chr15:41581600-41589400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:41581600-41589800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr15:41581600-41590800	Weak transcription	Osteobl	bone
45	chr15:41581600-41592200	Weak transcription	NH-A	brain
46	chr15:41581600-41601800	Weak transcription	Fetal Lung	lung
47	chr15:41581600-41623600	Weak transcription	Fetal Kidney	kidney
48	chr15:41581800-41589000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr15:41581800-41589000	Weak transcription	Left Ventricle	heart
50	chr15:41581800-41591600	Strong transcription	Fetal Intestine Small	intestine

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