Variant report

Variant	rs4592624
Chromosome Location	chr15:41389388-41389389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41377305..41379555-chr15:41389039..41391103,2	MCF-7	breast:
2	chr15:41389225..41391040-chr15:41407409..41409110,2	K562	blood:
3	chr15:41388020..41390130-chr15:41405775..41409320,4	K562	blood:

Variant related genes	Relation type
ENSG00000128908	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1009913	0.83[ASN][1000 genomes]
rs11853192	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11854472	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11855797	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856572	0.89[ASN][1000 genomes]
rs11856577	0.85[ASN][1000 genomes]
rs11856848	0.97[ASN][1000 genomes]
rs11858678	0.83[EUR][1000 genomes]
rs12101934	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12324159	0.84[EUR][1000 genomes]
rs1659227	0.83[EUR][1000 genomes]
rs1678750	0.97[ASN][1000 genomes]
rs1717200	0.84[ASN][1000 genomes]
rs1983400	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2176998	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2306083	0.89[ASN][1000 genomes]
rs2412601	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2578655	0.84[EUR][1000 genomes]
rs28409432	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28455998	0.90[ASN][1000 genomes]
rs28510775	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28516683	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28613002	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28664602	0.89[AFR][1000 genomes]
rs28688742	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28729675	0.90[ASN][1000 genomes]
rs28828670	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28866311	0.88[ASN][1000 genomes]
rs2899013	0.82[EUR][1000 genomes]
rs2928148	0.97[ASN][1000 genomes]
rs2928156	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2947493	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2947494	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3101442	0.87[ASN][1000 genomes]
rs36046988	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs476633	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516156	0.96[ASN][1000 genomes]
rs537244	0.83[EUR][1000 genomes]
rs544744	0.97[ASN][1000 genomes]
rs551482	0.83[EUR][1000 genomes]
rs561301	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57393155	0.91[ASN][1000 genomes]
rs61203391	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6492983	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66818965	0.97[ASN][1000 genomes]
rs690733	0.83[EUR][1000 genomes]
rs691672	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs691702	0.83[EUR][1000 genomes]
rs691830	0.86[ASN][1000 genomes]
rs692153	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs692195	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7170049	0.82[EUR][1000 genomes]
rs7173841	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7179681	0.85[ASN][1000 genomes]
rs7180853	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7181816	0.97[ASN][1000 genomes]
rs8023345	0.81[ASN][1000 genomes]
rs8027932	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033435	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8037837	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs8042088	0.83[ASN][1000 genomes]
rs9888710	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9888718	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9972349	0.82[EUR][1000 genomes]
rs9972622	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
2	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv569230	chr15:41384649-41483682	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv904108	chr15:41384649-41486990	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4592624	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41355000-41389400	Strong transcription	Placenta	Placenta
2	chr15:41355000-41392000	Strong transcription	Fetal Thymus	thymus
3	chr15:41355000-41392400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:41355000-41393800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:41355400-41390200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:41355400-41393200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:41355600-41390800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:41355800-41391000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:41356800-41391000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:41356800-41392200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:41358000-41393600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:41358200-41392000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:41361200-41407200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:41365200-41391000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:41365400-41389800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr15:41369000-41391800	Weak transcription	Right Atrium	heart
17	chr15:41370800-41390800	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr15:41371800-41390800	Weak transcription	Stomach Mucosa	stomach
19	chr15:41372800-41392400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:41373200-41389800	Strong transcription	Primary B cells from cord blood	blood
21	chr15:41375800-41389800	Strong transcription	HSMM	muscle
22	chr15:41378000-41397600	Weak transcription	Small Intestine	intestine
23	chr15:41380400-41393400	Strong transcription	Fetal Intestine Small	intestine
24	chr15:41383200-41406800	Weak transcription	A549	lung
25	chr15:41383800-41407400	Weak transcription	Esophagus	oesophagus
26	chr15:41384000-41407400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:41384200-41391400	Strong transcription	Hela-S3	cervix
28	chr15:41384200-41395600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:41384400-41396000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:41384400-41396000	Weak transcription	Psoas Muscle	Psoas
31	chr15:41384400-41407400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:41385200-41406000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:41386200-41398400	Weak transcription	Gastric	stomach
34	chr15:41386200-41407400	Weak transcription	Aorta	Aorta
35	chr15:41386400-41389400	Strong transcription	NHDF-Ad	bronchial
36	chr15:41386600-41407400	Weak transcription	Colonic Mucosa	Colon
37	chr15:41386800-41390400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:41386800-41396400	Weak transcription	Fetal Brain Male	brain
39	chr15:41386800-41398200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:41386800-41398400	Weak transcription	Brain Angular Gyrus	brain
41	chr15:41386800-41405400	Weak transcription	Spleen	Spleen
42	chr15:41386800-41406800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr15:41386800-41406800	Weak transcription	Right Ventricle	heart
44	chr15:41386800-41407000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr15:41386800-41407200	Weak transcription	HSMMtube	muscle
46	chr15:41386800-41407400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:41387000-41398200	Weak transcription	Lung	lung
48	chr15:41387000-41400400	Weak transcription	Brain Germinal Matrix	brain
49	chr15:41387200-41395200	Weak transcription	Brain Substantia Nigra	brain
50	chr15:41387200-41399200	Weak transcription	GM12878-XiMat	blood

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