Variant report

Variant	rs316605
Chromosome Location	chr15:41771591-41771592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41767730..41772843-chr15:41782564..41789351,11	K562	blood:

Variant related genes	Relation type
ENSG00000137825	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10152497	0.81[ASN][1000 genomes]
rs10153010	0.81[ASN][1000 genomes]
rs10467974	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs10518718	0.93[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs11630191	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11631770	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11633799	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap]
rs13379756	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs1622914	0.83[EUR][1000 genomes]
rs1655556	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1655557	0.86[EUR][1000 genomes]
rs16971767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs16971798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16971806	0.93[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs16971832	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16971834	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1757455	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757456	0.84[CEU][hapmap];0.80[CHB][hapmap];0.80[EUR][1000 genomes]
rs1757463	0.87[CHB][hapmap];0.85[LWK][hapmap]
rs2015781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs2026946	0.80[EUR][1000 genomes]
rs2777491	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]
rs28393472	0.81[ASN][1000 genomes]
rs28526381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs28557159	0.94[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs28600680	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28655070	0.88[ASN][1000 genomes]
rs28716108	0.81[ASN][1000 genomes]
rs28792672	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28847691	0.91[ASN][1000 genomes]
rs316609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs316610	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316613	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316614	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316615	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316617	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs35826725	0.93[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3743038	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59590312	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66538814	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66591771	0.80[EUR][1000 genomes]
rs7163788	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7167498	0.93[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs7167729	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7168177	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7168307	0.88[ASW][hapmap];0.80[GIH][hapmap]
rs7172148	0.87[ASN][1000 genomes]
rs7175800	0.93[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7176588	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs7177641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7178634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs7178777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs7180418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs7180492	0.96[ASN][1000 genomes]
rs7181911	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7182667	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7182700	0.89[EUR][1000 genomes]
rs73404994	0.81[ASN][1000 genomes]
rs73404995	0.81[ASN][1000 genomes]
rs73404996	0.81[ASN][1000 genomes]
rs73407109	0.81[ASN][1000 genomes]
rs8023530	0.89[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs8024774	0.84[CEU][hapmap];0.80[CHB][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs8026197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8027626	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8032838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs8034819	0.84[ASN][1000 genomes]
rs8036498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs8036527	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	0.89[ASW][hapmap];0.81[GIH][hapmap]
rs8037824	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8041325	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs823716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9302109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs9972288	0.85[EUR][1000 genomes];0.82[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	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
2	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs316605	NDUFAF1	cis	multi-tissue	Pritchard
rs316605	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs316605	OIP5-AS1	cis	Artery Tibial	GTEx
rs316605	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs316605	NDUFAF1	cis	Muscle Skeletal	GTEx
rs316605	NUSAP1	cis	parietal	SCAN
rs316605	NDUFAF1	cis	cerebellum	SCAN
rs316605	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs316605	OIP5-AS1	cis	Nerve Tibial	GTEx
rs316605	NUSAP1	cis	cerebellum	SCAN
rs316605	STARD9	cis	cerebellum	SCAN
rs316605	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs316605	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs316605	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs316605	NDUFAF1	cis	Thyroid	GTEx
rs316605	NDUFAF1	cis	parietal	SCAN
rs316605	RPAP1	cis	parietal	SCAN
rs316605	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs316605	NDUFAF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41724200-41777200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41729200-41773000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:41744000-41771800	Strong transcription	Fetal Intestine Small	intestine
4	chr15:41745200-41775800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr15:41753000-41775000	Strong transcription	Fetal Stomach	stomach
6	chr15:41753800-41776800	Strong transcription	Fetal Muscle Leg	muscle
7	chr15:41754000-41774400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:41754200-41775200	Strong transcription	Primary T cells from cord blood	blood
9	chr15:41754200-41776000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:41754400-41774600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:41754400-41775000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:41754400-41776800	Strong transcription	Placenta	Placenta
13	chr15:41755000-41775600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr15:41755400-41775200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:41756800-41776200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr15:41757000-41774200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:41757000-41776200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:41757000-41776400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:41757200-41774400	Strong transcription	Fetal Brain Female	brain
20	chr15:41757200-41774600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:41757200-41775400	Strong transcription	Fetal Thymus	thymus
22	chr15:41757400-41774000	Strong transcription	Spleen	Spleen
23	chr15:41757400-41774200	Strong transcription	Thymus	Thymus
24	chr15:41757400-41776800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr15:41758400-41774000	Strong transcription	Lung	lung
26	chr15:41759000-41772400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:41759000-41774400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:41759000-41775000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:41760600-41774000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:41760600-41774400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr15:41760800-41773800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:41760800-41775600	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr15:41761000-41776400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:41761200-41771600	Strong transcription	Fetal Intestine Large	intestine
35	chr15:41761200-41774400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:41761800-41772600	Strong transcription	Fetal Kidney	kidney
37	chr15:41762000-41776000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:41762200-41773600	Strong transcription	Colon Smooth Muscle	Colon
39	chr15:41762200-41773800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:41764600-41775800	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr15:41764800-41776000	Strong transcription	Fetal Lung	lung
42	chr15:41765000-41773200	Strong transcription	Hela-S3	cervix
43	chr15:41765000-41774000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr15:41765000-41774800	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr15:41765000-41774800	Strong transcription	Brain Cingulate Gyrus	brain
46	chr15:41765000-41777200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr15:41765200-41775400	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:41765400-41773000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr15:41765400-41773000	Strong transcription	GM12878-XiMat	blood
50	chr15:41765400-41773800	Strong transcription	Rectal Smooth Muscle	rectum

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