Variant report

Variant	rs2777491
Chromosome Location	chr15:41735710-41735711
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41732368..41735253-chr15:41735340..41739349,3	K562	blood:
2	chr15:41730144..41732034-chr15:41734170..41736991,2	K562	blood:

Extended variants
information (count: 100 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10152497	0.88[ASN][1000 genomes]
rs10153010	0.88[ASN][1000 genomes]
rs10467974	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs10518718	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11630191	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631770	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633799	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs12324291	0.86[ASN][1000 genomes]
rs13379756	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap]
rs1655556	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1655557	0.82[EUR][1000 genomes]
rs16971767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16971798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16971806	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16971832	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs16971834	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1757455	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757456	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs1757463	0.87[CHB][hapmap];0.85[LWK][hapmap]
rs2015781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28393472	0.88[ASN][1000 genomes]
rs28526381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs28557159	0.88[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs28578057	0.86[ASN][1000 genomes]
rs28583065	0.86[ASN][1000 genomes]
rs28600680	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28643296	0.82[ASN][1000 genomes]
rs28655070	0.91[ASN][1000 genomes]
rs28716108	0.88[ASN][1000 genomes]
rs28792672	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28847691	0.88[ASN][1000 genomes]
rs316605	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316610	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316613	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316614	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316615	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316617	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs35826725	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3743038	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55782852	0.86[ASN][1000 genomes]
rs58910172	0.82[ASN][1000 genomes]
rs59590312	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61037359	0.85[ASN][1000 genomes]
rs61127691	0.82[ASN][1000 genomes]
rs6650519	0.83[ASN][1000 genomes]
rs66538814	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66591771	0.85[EUR][1000 genomes]
rs7161772	0.86[ASN][1000 genomes]
rs7163649	0.85[ASN][1000 genomes]
rs7163788	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7165675	0.86[ASN][1000 genomes]
rs7167498	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7167729	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7168177	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7168307	0.83[ASW][hapmap];0.80[GIH][hapmap]
rs7172148	0.92[ASN][1000 genomes]
rs7175690	0.82[ASN][1000 genomes]
rs7175800	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7176314	0.82[ASN][1000 genomes]
rs7176588	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]
rs7177641	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7178777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7180418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7180492	0.83[ASN][1000 genomes]
rs7181560	0.81[ASN][1000 genomes]
rs7181911	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7182667	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7182700	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73404987	0.83[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[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs8024774	0.84[CEU][hapmap];0.80[CHB][hapmap];0.86[TSI][hapmap]
rs8026197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8027626	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8032838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs8034626	0.83[ASN][1000 genomes]
rs8034819	0.92[ASN][1000 genomes]
rs8036498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs8036527	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8037574	0.83[ASW][hapmap];0.81[GIH][hapmap]
rs8037824	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8041325	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs823716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs919961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9302109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs9672866	0.84[ASN][1000 genomes]
rs9972288	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2777491	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs2777491	NDUFAF1	cis	parietal	SCAN
rs2777491	OIP5-AS1	cis	Artery Tibial	GTEx
rs2777491	NDUFAF1	cis	cerebellum	SCAN
rs2777491	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs2777491	NUSAP1	cis	parietal	SCAN
rs2777491	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs2777491	NUSAP1	cis	cerebellum	SCAN
rs2777491	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs2777491	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs2777491	NDUFAF1	cis	multi-tissue	Pritchard
rs2777491	OIP5-AS1	cis	Nerve Tibial	GTEx
rs2777491	NDUFAF1	cis	Muscle Skeletal	GTEx
rs2777491	RPAP1	cis	parietal	SCAN
rs2777491	STARD9	cis	cerebellum	SCAN
rs2777491	NDUFAF1	cis	lymphoblastoid	seeQTL
rs2777491	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs2777491	NDUFAF1	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41710400-41745200	Weak transcription	Esophagus	oesophagus
2	chr15:41710400-41750000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41710600-41745200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:41711600-41746800	Weak transcription	A549	lung
5	chr15:41711600-41759000	Weak transcription	Fetal Heart	heart
6	chr15:41713200-41745200	Weak transcription	Spleen	Spleen
7	chr15:41718200-41745200	Weak transcription	Pancreas	Pancrea
8	chr15:41719000-41745200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:41719000-41749800	Weak transcription	NHLF	lung
10	chr15:41719000-41765800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:41721600-41745200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:41722000-41749200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:41722000-41749600	Weak transcription	Gastric	stomach
14	chr15:41722000-41768400	Weak transcription	Small Intestine	intestine
15	chr15:41724200-41777200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:41728200-41749800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:41729200-41773000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:41729400-41756200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:41729600-41736000	Strong transcription	Dnd41	blood
20	chr15:41729800-41735800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:41729800-41735800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr15:41729800-41736000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr15:41729800-41736000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:41729800-41736000	Strong transcription	Liver	Liver
25	chr15:41729800-41736000	Strong transcription	Placenta	Placenta
26	chr15:41729800-41736000	Strong transcription	Thymus	Thymus
27	chr15:41729800-41740400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:41730000-41768400	Weak transcription	Psoas Muscle	Psoas
29	chr15:41730200-41735800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr15:41730200-41736000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:41730200-41736000	Strong transcription	Fetal Intestine Large	intestine
32	chr15:41730200-41736000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:41730200-41736000	Strong transcription	Fetal Muscle Leg	muscle
34	chr15:41730200-41736200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:41730400-41735800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:41730400-41736000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr15:41730400-41736000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:41730400-41736600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:41730400-41736600	Strong transcription	Fetal Intestine Small	intestine
40	chr15:41730400-41738600	Strong transcription	Fetal Stomach	stomach
41	chr15:41730400-41749800	Weak transcription	Brain Substantia Nigra	brain
42	chr15:41730600-41735800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:41730600-41736000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:41730600-41736000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:41730600-41736800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:41730600-41746800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr15:41730800-41736000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:41730800-41769000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:41731000-41736600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:41731400-41735800	Strong transcription	HUES48 Cell Line	embryonic stem cell

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