Variant report

Variant	rs2925343
Chromosome Location	chr15:41306493-41306494
allele	C/T
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	RELA	chr15:41305878-41306524	GM12878	blood:	n/a	chr15:41306077-41306086 chr15:41306077-41306086
2	SPI1	chr15:41305889-41306625	GM12878	blood:	n/a	chr15:41306187-41306194 chr15:41306184-41306197

No.	Distal block	Cell Line	Cell type
1	chr15:41304575..41306936-chr15:41309313..41310862,2	MCF-7	breast:
2	chr15:41220910..41223038-chr15:41305571..41307390,2	K562	blood:
3	chr15:41302332..41304841-chr15:41304944..41307775,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259521	TF binding region
ENSG00000128917	Chromatin interaction
ENSG00000259463	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1001341	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1009913	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11855248	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11856572	0.84[ASN][1000 genomes]
rs11856848	0.84[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs12899590	0.93[ASN][1000 genomes]
rs12905926	0.96[ASN][1000 genomes]
rs12910027	0.96[ASN][1000 genomes]
rs13329511	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678750	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs1869907	0.84[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1962410	0.84[ASN][1000 genomes]
rs2305656	0.95[CEU][hapmap]
rs2306083	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2412572	0.90[ASN][1000 genomes]
rs2412574	0.88[ASN][1000 genomes]
rs28473405	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28479904	0.93[ASN][1000 genomes]
rs28501589	0.96[ASN][1000 genomes]
rs28550294	0.81[EUR][1000 genomes]
rs28572344	0.83[ASN][1000 genomes]
rs28581803	0.86[ASN][1000 genomes]
rs2925342	0.96[ASN][1000 genomes]
rs2925345	0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2925346	0.95[ASN][1000 genomes]
rs2927061	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2927062	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3100807	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3101436	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3214068	0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3900905	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3986311	0.90[ASN][1000 genomes]
rs4244584	0.89[ASN][1000 genomes]
rs4497658	0.90[ASN][1000 genomes]
rs476633	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4923890	0.88[ASN][1000 genomes]
rs4924528	0.80[ASN][1000 genomes]
rs4924532	0.86[ASN][1000 genomes]
rs6492978	0.85[ASN][1000 genomes]
rs692153	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs7162992	0.96[ASN][1000 genomes]
rs7169375	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7171437	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175269	0.85[MEX][hapmap];0.89[TSI][hapmap]
rs7179681	0.81[ASN][1000 genomes]
rs72737704	0.96[ASN][1000 genomes]
rs8023345	0.83[ASN][1000 genomes]
rs8030306	0.88[ASN][1000 genomes]
rs8042088	0.84[ASN][1000 genomes]
rs9920619	0.84[AMR][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2925343	RASGRP1	cis	parietal	SCAN
rs2925343	SPINT1	cis	cerebellum	SCAN
rs2925343	NUSAP1	cis	cerebellum	SCAN
rs2925343	C15orf62	cis	parietal	SCAN
rs2925343	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs2925343	GPR176	cis	cerebellum	SCAN
rs2925343	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs2925343	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs2925343	NDUFAF1	cis	parietal	SCAN
rs2925343	OIP5-AS1	cis	Artery Tibial	GTEx
rs2925343	NDUFAF1	cis	lymphoblastoid	seeQTL
rs2925343	NDUFAF1	cis	Muscle Skeletal	GTEx
rs2925343	GPR176	cis	parietal	SCAN

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	chr15:41276600-41354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41280200-41306600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:41280400-41339800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:41288200-41307400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:41288200-41309800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:41289200-41306800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:41289400-41307000	Weak transcription	Colonic Mucosa	Colon
9	chr15:41289800-41307800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:41289800-41310600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:41290000-41308200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:41290200-41310600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:41293800-41308400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:41294000-41308200	Weak transcription	Gastric	stomach
15	chr15:41294000-41310600	Weak transcription	Psoas Muscle	Psoas
16	chr15:41294000-41313000	Weak transcription	Esophagus	oesophagus
17	chr15:41294000-41314600	Weak transcription	Aorta	Aorta
18	chr15:41294000-41316600	Weak transcription	Pancreas	Pancrea
19	chr15:41294200-41316800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:41296000-41310200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:41296000-41315600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:41296400-41308200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:41296400-41308200	Weak transcription	Right Ventricle	heart
24	chr15:41297000-41306600	Weak transcription	Brain Germinal Matrix	brain
25	chr15:41297000-41306600	Weak transcription	HSMMtube	muscle
26	chr15:41297000-41307400	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:41297000-41307800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:41297000-41309400	Weak transcription	Brain Anterior Caudate	brain
29	chr15:41297200-41307800	Weak transcription	Thymus	Thymus
30	chr15:41297200-41308200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr15:41297400-41308400	Weak transcription	Fetal Brain Female	brain
32	chr15:41297400-41310800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:41297600-41308400	Weak transcription	Brain Angular Gyrus	brain
34	chr15:41298000-41306800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:41298000-41306800	Weak transcription	Left Ventricle	heart
36	chr15:41298000-41307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:41298000-41308200	Weak transcription	Spleen	Spleen
38	chr15:41298200-41306800	Weak transcription	HMEC	breast
39	chr15:41300200-41322400	Strong transcription	Primary T cells from cord blood	blood
40	chr15:41300600-41307800	Weak transcription	Lung	lung
41	chr15:41300800-41308200	Weak transcription	Brain Substantia Nigra	brain
42	chr15:41301200-41307600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:41301400-41308200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:41301600-41307800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:41301600-41313800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:41301800-41315600	Strong transcription	Dnd41	blood
47	chr15:41302200-41307600	Weak transcription	Fetal Stomach	stomach
48	chr15:41302200-41315600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr15:41302200-41315800	Strong transcription	K562	blood
50	chr15:41302800-41314000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links