Variant report

Variant	rs3101436
Chromosome Location	chr15:41287689-41287690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41285579..41288391-chr15:41288510..41290636,2	K562	blood:
2	chr15:41281416..41284789-chr15:41286455..41289587,3	K562	blood:
3	chr15:41225668..41227259-chr15:41286163..41288486,2	K562	blood:

Variant related genes	Relation type
ENSG00000128908	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1001341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1009913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070315	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11070317	0.83[EUR][1000 genomes]
rs11854472	0.85[EUR][1000 genomes]
rs11855248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856572	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11856577	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11856848	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11858678	0.86[MEX][hapmap]
rs12899590	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905926	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910027	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329511	0.96[ASN][1000 genomes]
rs1678750	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap]
rs1717200	0.81[EUR][1000 genomes]
rs1869907	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1962410	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1983400	0.80[ASN][1000 genomes]
rs2306083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2412572	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412574	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28473405	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28479904	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28501589	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28572344	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28581803	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899002	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2925342	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2925343	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2925345	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2925346	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2927061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2927062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2947493	0.80[ASN][1000 genomes]
rs2947494	0.80[ASN][1000 genomes]
rs3100807	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3214068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3900905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3986311	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4244584	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4497658	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs476633	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4923890	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924519	0.83[EUR][1000 genomes]
rs4924522	0.81[EUR][1000 genomes]
rs4924525	0.85[EUR][1000 genomes]
rs4924528	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924532	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs516156	0.81[EUR][1000 genomes]
rs544744	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6492978	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs690733	0.86[MEX][hapmap]
rs692153	0.94[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs692155	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs7162992	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171437	0.96[ASN][1000 genomes]
rs7179681	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7181816	0.85[EUR][1000 genomes]
rs72737704	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8023345	0.87[ASN][1000 genomes]
rs8030306	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8042088	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9796	0.96[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053462	chr15:41270067-41396094	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3101436	NDUFAF1	cis	lymphoblastoid	seeQTL
rs3101436	NDUFAF1	cis	parietal	SCAN
rs3101436	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41258800-41348400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:41266800-41290000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:41266800-41298400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:41267200-41294800	Strong transcription	Primary T cells from cord blood	blood
5	chr15:41267600-41294200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:41267600-41301200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:41267800-41290200	Strong transcription	NHEK	skin
8	chr15:41267800-41290800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:41267800-41294200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:41267800-41301400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:41268000-41290200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:41268000-41292800	Strong transcription	Liver	Liver
13	chr15:41268000-41294800	Strong transcription	Fetal Thymus	thymus
14	chr15:41268000-41298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:41268000-41302400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr15:41268200-41290200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:41268200-41295000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr15:41268600-41289800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr15:41276200-41296000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:41276600-41290800	Weak transcription	Psoas Muscle	Psoas
21	chr15:41276600-41354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:41276800-41293600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:41276800-41305200	Weak transcription	Fetal Brain Male	brain
24	chr15:41277600-41290000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:41278000-41287800	Weak transcription	Gastric	stomach
26	chr15:41278000-41294800	Strong transcription	Fetal Muscle Leg	muscle
27	chr15:41278400-41290000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:41278600-41287800	Weak transcription	Right Ventricle	heart
29	chr15:41279600-41288000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:41279600-41293400	Weak transcription	Small Intestine	intestine
31	chr15:41279600-41293400	Weak transcription	Stomach Mucosa	stomach
32	chr15:41279800-41298200	Weak transcription	Fetal Heart	heart
33	chr15:41280000-41288000	Weak transcription	Colonic Mucosa	Colon
34	chr15:41280200-41293600	Weak transcription	Aorta	Aorta
35	chr15:41280200-41306600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr15:41280400-41288000	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:41280400-41288800	Weak transcription	Brain Substantia Nigra	brain
38	chr15:41280400-41339800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr15:41280800-41288000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:41281400-41290000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:41281600-41290200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr15:41282400-41290000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:41282400-41290200	Strong transcription	HepG2	liver
44	chr15:41282400-41295200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:41282600-41290000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr15:41282600-41293400	Strong transcription	Left Ventricle	heart
47	chr15:41282800-41290400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr15:41283400-41287800	Weak transcription	Brain Angular Gyrus	brain
49	chr15:41283400-41290200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:41283600-41292800	Strong transcription	Sigmoid Colon	Sigmoid Colon

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