Variant report

Variant	rs13379756
Chromosome Location	chr15:41663896-41663897
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10152497	0.96[ASN][1000 genomes]
rs10153010	0.96[ASN][1000 genomes]
rs10467974	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10518718	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11630191	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631770	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11633799	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11852609	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11857631	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12324291	0.93[ASN][1000 genomes]
rs1655556	0.83[EUR][1000 genomes]
rs16971767	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16971798	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16971806	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16971832	0.91[JPT][hapmap]
rs16971834	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs1757455	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757456	0.80[CHB][hapmap]
rs1757463	0.87[CHB][hapmap]
rs2015781	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777491	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28393472	0.96[ASN][1000 genomes]
rs28526381	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28557159	0.90[GIH][hapmap]
rs28578057	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28583065	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28600680	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28643296	0.89[ASN][1000 genomes]
rs28655070	0.88[ASN][1000 genomes]
rs28716108	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28792672	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28847691	0.85[ASN][1000 genomes]
rs316605	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs316609	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316610	0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs316613	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316614	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316615	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316617	0.87[CHB][hapmap];0.84[TSI][hapmap]
rs35826725	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3743038	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55782852	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58335029	0.85[ASN][1000 genomes]
rs58910172	0.89[ASN][1000 genomes]
rs59590312	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61037359	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61127691	0.89[ASN][1000 genomes]
rs6650519	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66538814	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161772	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7163649	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7163788	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165675	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7167498	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7167729	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7168177	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7168307	0.90[GIH][hapmap]
rs7172148	0.89[ASN][1000 genomes]
rs7175690	0.89[ASN][1000 genomes]
rs7175800	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7176314	0.89[ASN][1000 genomes]
rs7176505	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7176588	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];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7177641	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7178634	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap]
rs7178777	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap]
rs7180418	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap]
rs7180492	0.80[ASN][1000 genomes]
rs7181560	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7181911	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182667	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182700	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7183337	0.85[ASN][1000 genomes]
rs73404980	0.85[ASN][1000 genomes]
rs73404987	0.91[ASN][1000 genomes]
rs73404994	0.96[ASN][1000 genomes]
rs73404995	0.96[ASN][1000 genomes]
rs73404996	0.96[ASN][1000 genomes]
rs73405000	0.93[ASN][1000 genomes]
rs73405001	0.93[ASN][1000 genomes]
rs73407109	0.96[ASN][1000 genomes]
rs8023530	0.90[GIH][hapmap]
rs8023619	0.85[ASN][1000 genomes]
rs8024774	0.80[CHB][hapmap];0.83[TSI][hapmap]
rs8026197	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8027626	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8032838	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8034626	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8034819	0.89[ASN][1000 genomes]
rs8036498	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8036527	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8037574	0.90[GIH][hapmap]
rs8037824	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041325	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap]
rs823716	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs919961	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9302109	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672866	0.92[ASN][1000 genomes]
rs9972288	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs13379756	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs13379756	NDUFAF1	cis	cerebellum	SCAN
rs13379756	OIP5-AS1	cis	Nerve Tibial	GTEx
rs13379756	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs13379756	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs13379756	RPAP1	cis	parietal	SCAN
rs13379756	CASC5	cis	cerebellum	SCAN
rs13379756	NUSAP1	cis	cerebellum	SCAN
rs13379756	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs13379756	NDUFAF1	cis	parietal	SCAN
rs13379756	NDUFAF1	cis	multi-tissue	Pritchard
rs13379756	NUSAP1	cis	parietal	SCAN
rs13379756	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs13379756	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs13379756	OIP5-AS1	cis	Esophagus Muscularis	GTEx
rs13379756	NDUFAF1	cis	Muscle Skeletal	GTEx
rs13379756	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs13379756	NDUFAF1	cis	lymphoblastoid	seeQTL
rs13379756	OIP5-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41625400-41670200	Weak transcription	Gastric	stomach
2	chr15:41625800-41665800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:41625800-41694200	Weak transcription	Small Intestine	intestine
4	chr15:41626000-41665200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:41626200-41678200	Weak transcription	Liver	Liver
6	chr15:41626200-41680200	Weak transcription	Fetal Brain Male	brain
7	chr15:41626400-41677800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:41626400-41678400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:41626800-41686400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:41627000-41672800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:41627200-41676800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:41627400-41668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr15:41627400-41673000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:41628200-41673000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:41628600-41672800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:41628600-41673800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:41629000-41672000	Weak transcription	Primary T cells from cord blood	blood
18	chr15:41629000-41673000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:41629400-41672400	Strong transcription	Fetal Stomach	stomach
20	chr15:41629400-41672800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:41629400-41673600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:41629600-41674000	Strong transcription	Fetal Thymus	thymus
23	chr15:41630400-41674000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:41630400-41674200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr15:41630800-41673800	Strong transcription	Dnd41	blood
26	chr15:41631800-41679200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:41632000-41673000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:41632000-41673600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:41632200-41674000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:41632800-41673800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:41639200-41671800	Strong transcription	Hela-S3	cervix
32	chr15:41640800-41674000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:41642800-41679400	Weak transcription	Ovary	ovary
34	chr15:41643800-41679000	Weak transcription	Pancreas	Pancrea
35	chr15:41644000-41670200	Weak transcription	Placenta	Placenta
36	chr15:41644200-41678600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr15:41644200-41679800	Weak transcription	Primary B cells from cord blood	blood
38	chr15:41650600-41673600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr15:41653800-41665000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr15:41653800-41665000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr15:41654200-41678200	Weak transcription	HSMMtube	muscle
42	chr15:41655400-41674000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:41655600-41673800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:41655600-41673800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:41655800-41672000	Strong transcription	Fetal Intestine Small	intestine
46	chr15:41656000-41673200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:41656800-41665400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:41656800-41666600	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:41656800-41668200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:41656800-41669400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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