Variant report

Variant	rs2927062
Chromosome Location	chr15:41302687-41302688
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	CTCF	chr15:41302650-41302793	HepG2	liver:	n/a	n/a
2	RAD21	chr15:41302634-41302816	SK-N-SH_RA	brain:	n/a	n/a
3	RAD21	chr15:41302625-41302810	HepG2	liver:	n/a	n/a
4	CTCF	chr15:41302669-41302757	MCF-7	breast:	n/a	n/a
5	CTCF	chr15:41302625-41302793	HepG2	liver:	n/a	n/a
6	CTCF	chr15:41302653-41302775	MCF-7	breast:	n/a	n/a
7	RAD21	chr15:41302532-41302860	HepG2	liver:	n/a	n/a
8	CTCF	chr15:41302560-41302710	BE2_C	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41221498..41223245-chr15:41301419..41303112,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259463	TF binding region
ENSG00000128917	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1001341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1009913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070315	1.00[CEU][hapmap]
rs11854472	0.86[EUR][1000 genomes]
rs11855248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856572	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11856577	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11856848	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11858678	0.86[MEX][hapmap]
rs12899590	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12905926	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12910027	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13329511	0.96[ASN][1000 genomes]
rs1678750	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs1717200	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1869907	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1962410	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1983400	0.80[AFR][1000 genomes]
rs2306083	1.00[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];0.86[ASN][1000 genomes]
rs2412572	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2412574	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28473405	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28479904	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28501589	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28572344	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28581803	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2899002	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2925342	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925343	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2925345	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2925346	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2927061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3100807	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]
rs3101436	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]
rs3214068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3900905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3986311	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4244584	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4497658	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs4923890	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924519	0.80[EUR][1000 genomes]
rs4924525	0.82[EUR][1000 genomes]
rs4924528	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924532	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs516156	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs544744	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6492978	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690733	0.86[MEX][hapmap]
rs692153	0.94[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs692155	0.96[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap]
rs7162992	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7169375	1.00[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];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171437	0.96[ASN][1000 genomes]
rs7179681	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7181816	0.86[EUR][1000 genomes]
rs72737704	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023345	0.85[ASN][1000 genomes]
rs8030306	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8042088	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9796	0.96[CEU][hapmap];0.82[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
rs2927062	NDUFAF1	cis	lymphoblastoid	seeQTL
rs2927062	NDUFAF1	cis	parietal	SCAN

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	chr15:41276600-41354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41276800-41305200	Weak transcription	Fetal Brain Male	brain
4	chr15:41280200-41306600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:41280400-41339800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:41288200-41307400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:41288200-41309800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:41289200-41306800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:41289400-41307000	Weak transcription	Colonic Mucosa	Colon
10	chr15:41289800-41307800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:41289800-41310600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:41290000-41308200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:41290200-41310600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:41293800-41308400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:41294000-41303200	Weak transcription	Stomach Mucosa	stomach
16	chr15:41294000-41308200	Weak transcription	Gastric	stomach
17	chr15:41294000-41310600	Weak transcription	Psoas Muscle	Psoas
18	chr15:41294000-41313000	Weak transcription	Esophagus	oesophagus
19	chr15:41294000-41314600	Weak transcription	Aorta	Aorta
20	chr15:41294000-41316600	Weak transcription	Pancreas	Pancrea
21	chr15:41294200-41306200	Weak transcription	Fetal Kidney	kidney
22	chr15:41294200-41316800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:41294800-41303200	Weak transcription	Small Intestine	intestine
24	chr15:41295800-41306000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr15:41296000-41310200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:41296000-41315600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:41296400-41308200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:41296400-41308200	Weak transcription	Right Ventricle	heart
29	chr15:41296600-41306200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr15:41296800-41303600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:41297000-41303200	Weak transcription	NHEK	skin
32	chr15:41297000-41306400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:41297000-41306600	Weak transcription	Brain Germinal Matrix	brain
34	chr15:41297000-41306600	Weak transcription	HSMMtube	muscle
35	chr15:41297000-41307400	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:41297000-41307800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:41297000-41309400	Weak transcription	Brain Anterior Caudate	brain
38	chr15:41297200-41303600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:41297200-41303800	Weak transcription	A549	lung
40	chr15:41297200-41305200	Weak transcription	NH-A	brain
41	chr15:41297200-41306000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:41297200-41307800	Weak transcription	Thymus	Thymus
43	chr15:41297200-41308200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:41297400-41303200	Weak transcription	Brain Hippocampus Middle	brain
45	chr15:41297400-41303400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:41297400-41304800	Weak transcription	NHDF-Ad	bronchial
47	chr15:41297400-41308400	Weak transcription	Fetal Brain Female	brain
48	chr15:41297400-41310800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:41297600-41303400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:41297600-41308400	Weak transcription	Brain Angular Gyrus	brain

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