Variant report

Variant	rs2925346
Chromosome Location	chr15:41315695-41315696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41308637..41310191-chr15:41313089..41316074,2	MCF-7	breast:
2	chr15:41223425..41225650-chr15:41313290..41316160,2	MCF-7	breast:
3	chr15:41309782..41311326-chr15:41314850..41316484,2	K562	blood:
4	chr15:41220101..41221997-chr15:41315168..41317326,2	MCF-7	breast:
5	chr15:41314841..41316914-chr15:41624845..41626746,2	K562	blood:

Variant related genes	Relation type
ENSG00000259521	Chromatin interaction
ENSG00000137804	Chromatin interaction
ENSG00000128917	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1001341	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1009913	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11854472	0.87[EUR][1000 genomes]
rs11855248	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11856572	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11856577	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11856848	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12899590	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12905926	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910027	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13329511	0.95[ASN][1000 genomes]
rs1678750	0.82[EUR][1000 genomes]
rs1717200	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1869907	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1962410	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2306083	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412572	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2412574	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28473405	0.94[ASN][1000 genomes]
rs28479904	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28501589	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28572344	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28581803	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2925342	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2925343	0.95[ASN][1000 genomes]
rs2925345	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2927061	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2927062	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2928148	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2947493	0.81[AFR][1000 genomes]
rs3100807	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3101436	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3214068	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3900905	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3986311	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4244584	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4497658	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4923890	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924525	0.81[EUR][1000 genomes]
rs4924528	0.82[ASN][1000 genomes]
rs4924532	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs516156	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs544744	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6492978	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66818965	0.81[EUR][1000 genomes]
rs691830	0.81[EUR][1000 genomes]
rs692155	0.81[EUR][1000 genomes]
rs7162992	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7169375	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7171437	0.95[ASN][1000 genomes]
rs7179681	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7181816	0.87[EUR][1000 genomes]
rs72737704	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8023345	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8030306	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8042088	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9796	0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2925346	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr15:41280400-41339800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:41294000-41316600	Weak transcription	Pancreas	Pancrea
5	chr15:41294200-41316800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:41300200-41322400	Strong transcription	Primary T cells from cord blood	blood
7	chr15:41302200-41315800	Strong transcription	K562	blood
8	chr15:41303200-41320200	Strong transcription	Hela-S3	cervix
9	chr15:41303400-41321800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:41303400-41323400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:41303600-41318000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:41304200-41318000	Weak transcription	Small Intestine	intestine
13	chr15:41304800-41322200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:41306000-41322200	Strong transcription	Fetal Thymus	thymus
15	chr15:41306800-41316400	Weak transcription	Fetal Heart	heart
16	chr15:41306800-41338800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:41307600-41335000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:41308600-41316200	Weak transcription	NH-A	brain
19	chr15:41308800-41331200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:41308800-41337000	Weak transcription	Colonic Mucosa	Colon
21	chr15:41309000-41316200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:41309000-41339200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:41309200-41316600	Weak transcription	Ovary	ovary
24	chr15:41309400-41332600	Weak transcription	Gastric	stomach
25	chr15:41310000-41333200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:41310000-41333400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:41310200-41322400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr15:41310600-41316600	Weak transcription	Brain Germinal Matrix	brain
29	chr15:41311000-41319000	Weak transcription	Psoas Muscle	Psoas
30	chr15:41311000-41322200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr15:41311000-41328800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:41311200-41316200	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:41311200-41320000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr15:41311400-41335400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr15:41311600-41316600	Weak transcription	Stomach Mucosa	stomach
36	chr15:41311800-41318400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:41312000-41316400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:41312600-41315800	Genic enhancers	Osteobl	bone
39	chr15:41312800-41316200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:41312800-41318400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:41312800-41319000	Weak transcription	Spleen	Spleen
42	chr15:41313000-41316600	Weak transcription	Fetal Kidney	kidney
43	chr15:41313200-41316200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:41313200-41316400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:41313200-41316400	Weak transcription	NHDF-Ad	bronchial
46	chr15:41313200-41316800	Weak transcription	Thymus	Thymus
47	chr15:41313200-41319200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:41313400-41316400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:41313400-41316400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:41313400-41316400	Weak transcription	Stomach Smooth Muscle	stomach

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