Variant report

Variant	rs476633
Chromosome Location	chr15:41392134-41392135
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41391634..41395412-chr15:41405784..41409599,4	K562	blood:
2	chr15:41391907..41394522-chr15:41395092..41397540,2	K562	blood:
3	chr15:41391555..41394241-chr15:41403159..41405692,2	K562	blood:

Variant related genes	Relation type
ENSG00000128908	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1001341	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1009913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11853192	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11854472	0.97[ASN][1000 genomes]
rs11855102	0.82[CEU][hapmap]
rs11855248	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11855797	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856572	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11856577	0.85[ASN][1000 genomes]
rs11856848	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11858678	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12101934	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12324159	0.84[EUR][1000 genomes]
rs1659227	0.83[EUR][1000 genomes]
rs1678750	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1717200	0.84[ASN][1000 genomes]
rs1869907	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1983400	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2176998	0.93[ASN][1000 genomes]
rs2306083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2412601	0.90[ASN][1000 genomes]
rs2578655	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28409432	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28455998	0.90[ASN][1000 genomes]
rs28473405	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs28510775	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28516683	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28613002	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28688742	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28729675	0.90[ASN][1000 genomes]
rs28828670	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28866311	0.88[ASN][1000 genomes]
rs2899013	0.82[EUR][1000 genomes]
rs2918462	0.88[CEU][hapmap]
rs2925343	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2925345	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2927061	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2927062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2928148	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2928156	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2947493	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2947494	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3100807	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3101436	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3101442	0.87[ASN][1000 genomes]
rs3214068	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs36046988	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3900905	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4592624	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516156	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs537244	0.83[EUR][1000 genomes]
rs544744	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs551482	0.83[EUR][1000 genomes]
rs561301	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57393155	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs61203391	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6492982	0.86[AFR][1000 genomes]
rs6492983	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6492993	0.81[CEU][hapmap]
rs66818965	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs690733	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs691672	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs691702	0.83[EUR][1000 genomes]
rs691830	0.86[ASN][1000 genomes]
rs692153	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs692155	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs692195	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169375	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7170049	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs7173841	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7179681	0.85[ASN][1000 genomes]
rs7180853	0.84[AMR][1000 genomes];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[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033435	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8037837	0.96[ASN][1000 genomes]
rs8042088	0.83[ASN][1000 genomes]
rs8043253	0.81[CEU][hapmap]
rs909024	0.84[CHB][hapmap]
rs9888710	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9888718	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9972349	0.89[CEU][hapmap];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs476633	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs476633	CHP1	cis	Esophagus Mucosa	GTEx
rs476633	NDUFAF1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41355000-41392400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:41355000-41393800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:41355400-41393200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:41356800-41392200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:41358000-41393600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:41361200-41407200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:41372800-41392400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:41378000-41397600	Weak transcription	Small Intestine	intestine
9	chr15:41380400-41393400	Strong transcription	Fetal Intestine Small	intestine
10	chr15:41383200-41406800	Weak transcription	A549	lung
11	chr15:41383800-41407400	Weak transcription	Esophagus	oesophagus
12	chr15:41384000-41407400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:41384200-41395600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:41384400-41396000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:41384400-41396000	Weak transcription	Psoas Muscle	Psoas
16	chr15:41384400-41407400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:41385200-41406000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:41386200-41398400	Weak transcription	Gastric	stomach
19	chr15:41386200-41407400	Weak transcription	Aorta	Aorta
20	chr15:41386600-41407400	Weak transcription	Colonic Mucosa	Colon
21	chr15:41386800-41396400	Weak transcription	Fetal Brain Male	brain
22	chr15:41386800-41398200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:41386800-41398400	Weak transcription	Brain Angular Gyrus	brain
24	chr15:41386800-41405400	Weak transcription	Spleen	Spleen
25	chr15:41386800-41406800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:41386800-41406800	Weak transcription	Right Ventricle	heart
27	chr15:41386800-41407000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr15:41386800-41407200	Weak transcription	HSMMtube	muscle
29	chr15:41386800-41407400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:41387000-41398200	Weak transcription	Lung	lung
31	chr15:41387000-41400400	Weak transcription	Brain Germinal Matrix	brain
32	chr15:41387200-41395200	Weak transcription	Brain Substantia Nigra	brain
33	chr15:41387200-41399200	Weak transcription	GM12878-XiMat	blood
34	chr15:41387200-41406000	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:41387200-41406600	Weak transcription	Pancreas	Pancrea
36	chr15:41387400-41407200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:41388000-41394400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:41388000-41398400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:41388000-41406600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:41388200-41406600	Weak transcription	Adipose Nuclei	Adipose
41	chr15:41388400-41406400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:41388600-41395000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:41388600-41395000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:41388600-41395000	Weak transcription	Osteobl	bone
45	chr15:41388600-41396000	Weak transcription	HUVEC	blood vessel
46	chr15:41388600-41396200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:41388600-41398000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:41388600-41398400	Weak transcription	Left Ventricle	heart
49	chr15:41388600-41400200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:41388600-41400800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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