Variant report

Variant	rs2927061
Chromosome Location	chr15:41302219-41302220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41296826..41298405-chr15:41300610..41302274,2	K562	blood:
2	chr15:41221498..41223245-chr15:41301419..41303112,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128908	Chromatin interaction
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];1.00[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];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[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];0.81[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][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]
rs2927062	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];0.91[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]
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];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]
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]
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];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs692155	0.96[CEU][hapmap];0.85[CHB][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
rs2927061	NDUFAF1	cis	lymphoblastoid	seeQTL
rs2927061	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	chr15:41268000-41302400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr15:41276600-41354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:41276800-41305200	Weak transcription	Fetal Brain Male	brain
5	chr15:41280200-41306600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:41280400-41339800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:41288200-41307400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:41288200-41309800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:41289200-41306800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:41289400-41307000	Weak transcription	Colonic Mucosa	Colon
11	chr15:41289800-41307800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:41289800-41310600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:41290000-41308200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:41290200-41310600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:41293800-41308400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:41294000-41303200	Weak transcription	Stomach Mucosa	stomach
17	chr15:41294000-41308200	Weak transcription	Gastric	stomach
18	chr15:41294000-41310600	Weak transcription	Psoas Muscle	Psoas
19	chr15:41294000-41313000	Weak transcription	Esophagus	oesophagus
20	chr15:41294000-41314600	Weak transcription	Aorta	Aorta
21	chr15:41294000-41316600	Weak transcription	Pancreas	Pancrea
22	chr15:41294200-41306200	Weak transcription	Fetal Kidney	kidney
23	chr15:41294200-41316800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr15:41294800-41303200	Weak transcription	Small Intestine	intestine
25	chr15:41295800-41302400	Strong transcription	Fetal Muscle Leg	muscle
26	chr15:41295800-41306000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr15:41296000-41302400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:41296000-41310200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:41296000-41315600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:41296400-41308200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:41296400-41308200	Weak transcription	Right Ventricle	heart
32	chr15:41296600-41306200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:41296800-41303600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:41297000-41302600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:41297000-41303200	Weak transcription	NHEK	skin
36	chr15:41297000-41306400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:41297000-41306600	Weak transcription	Brain Germinal Matrix	brain
38	chr15:41297000-41306600	Weak transcription	HSMMtube	muscle
39	chr15:41297000-41307400	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:41297000-41307800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:41297000-41309400	Weak transcription	Brain Anterior Caudate	brain
42	chr15:41297200-41303600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:41297200-41303800	Weak transcription	A549	lung
44	chr15:41297200-41305200	Weak transcription	NH-A	brain
45	chr15:41297200-41306000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr15:41297200-41307800	Weak transcription	Thymus	Thymus
47	chr15:41297200-41308200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr15:41297400-41303200	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:41297400-41303400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:41297400-41304800	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links