Variant report

Variant	rs3100807
Chromosome Location	chr15:41292206-41292207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr15:41290510-41292276	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41292088..41294732-chr15:41407078..41409058,2	K562	blood:
2	chr15:41220148..41223426-chr15:41291682..41295350,3	K562	blood:

Variant related genes	Relation type
INO80	TF binding region
ENSG00000128908	Chromatin interaction
ENSG00000128917	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1001341	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1009913	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070315	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11070317	0.82[EUR][1000 genomes]
rs11854472	0.86[EUR][1000 genomes]
rs11855248	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856572	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11856577	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11856848	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11858678	0.86[MEX][hapmap]
rs12899590	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905926	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910027	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329511	0.96[ASN][1000 genomes]
rs1678750	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs1717200	0.82[EUR][1000 genomes]
rs1869907	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1962410	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1983400	0.80[ASN][1000 genomes]
rs2306083	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2412572	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412574	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28473405	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28479904	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28501589	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28572344	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28581803	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899002	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2925342	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2925343	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2925345	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2925346	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2927061	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2927062	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2947493	0.80[ASN][1000 genomes]
rs2947494	0.80[ASN][1000 genomes]
rs3101436	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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3900905	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3986311	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4244584	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4497658	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs476633	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4923890	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924519	0.82[EUR][1000 genomes]
rs4924522	0.80[EUR][1000 genomes]
rs4924525	0.84[EUR][1000 genomes]
rs4924528	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924532	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs516156	0.82[EUR][1000 genomes]
rs544744	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6492978	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs690733	0.86[MEX][hapmap]
rs692153	0.94[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs692155	0.91[CEU][hapmap];0.84[CHB][hapmap]
rs7162992	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169375	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171437	0.96[ASN][1000 genomes]
rs7179681	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7181816	0.86[EUR][1000 genomes]
rs72737704	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8023345	0.87[ASN][1000 genomes]
rs8030306	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8042088	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9796	0.91[CEU][hapmap];0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3100807	NDUFAF1	cis	parietal	SCAN
rs3100807	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr15:41266800-41298400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr15:41267200-41294800	Strong transcription	Primary T cells from cord blood	blood
4	chr15:41267600-41294200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:41267600-41301200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:41267800-41294200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:41267800-41301400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr15:41268000-41292800	Strong transcription	Liver	Liver
9	chr15:41268000-41294800	Strong transcription	Fetal Thymus	thymus
10	chr15:41268000-41298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:41268000-41302400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:41268200-41295000	Strong transcription	Primary B cells from peripheral blood	blood
13	chr15:41276200-41296000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:41276600-41354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:41276800-41293600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:41276800-41305200	Weak transcription	Fetal Brain Male	brain
17	chr15:41278000-41294800	Strong transcription	Fetal Muscle Leg	muscle
18	chr15:41279600-41293400	Weak transcription	Small Intestine	intestine
19	chr15:41279600-41293400	Weak transcription	Stomach Mucosa	stomach
20	chr15:41279800-41298200	Weak transcription	Fetal Heart	heart
21	chr15:41280200-41293600	Weak transcription	Aorta	Aorta
22	chr15:41280200-41306600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:41280400-41339800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:41282400-41295200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:41282600-41293400	Strong transcription	Left Ventricle	heart
26	chr15:41283600-41292800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:41284400-41301600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr15:41285800-41298600	Strong transcription	Dnd41	blood
29	chr15:41286000-41294000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:41286000-41294400	Strong transcription	Fetal Lung	lung
31	chr15:41286000-41298000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:41286000-41298200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:41286000-41299000	Strong transcription	Primary B cells from cord blood	blood
34	chr15:41286200-41293600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:41286200-41293600	Strong transcription	Adipose Nuclei	Adipose
36	chr15:41286200-41293800	Strong transcription	HSMMtube	muscle
37	chr15:41286200-41294000	Strong transcription	HSMM	muscle
38	chr15:41286200-41294800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:41286200-41294800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr15:41286400-41292600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:41286400-41293200	Strong transcription	Fetal Intestine Large	intestine
42	chr15:41286400-41298000	Strong transcription	Fetal Stomach	stomach
43	chr15:41287000-41292600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr15:41287200-41292800	Strong transcription	Fetal Intestine Small	intestine
45	chr15:41287200-41301000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:41287400-41293000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:41288200-41307400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr15:41288200-41309800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:41288400-41296000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:41288400-41296000	Weak transcription	K562	blood

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