Variant report

Variant	rs6492997
Chromosome Location	chr15:41541171-41541172
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41522934..41525087-chr15:41540802..41542732,2	K562	blood:
2	chr15:41522934..41525322-chr15:41540683..41542302,2	K562	blood:
3	chr15:41535934..41538302-chr15:41541101..41542958,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178997	Chromatin interaction
ENSG00000187446	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10152855	0.85[ASN][1000 genomes]
rs11855102	0.80[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858115	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858678	0.84[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes]
rs12324159	0.82[EUR][1000 genomes]
rs1659227	0.83[EUR][1000 genomes]
rs16971693	0.83[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs16971700	0.88[ASN][1000 genomes]
rs1866400	0.83[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1965139	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965140	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1971131	0.83[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs2083239	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2164996	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578655	0.82[EUR][1000 genomes]
rs28409265	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493237	0.85[ASN][1000 genomes]
rs28495204	0.85[ASN][1000 genomes]
rs28568756	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615543	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28665387	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28735224	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899013	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2918462	0.92[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap]
rs41442144	0.87[ASN][1000 genomes]
rs4258585	0.85[ASN][1000 genomes]
rs4419033	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4445868	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs494490	0.83[GIH][hapmap];0.85[TSI][hapmap]
rs537244	0.83[EUR][1000 genomes]
rs551482	0.83[EUR][1000 genomes]
rs55756301	0.83[ASN][1000 genomes]
rs56082289	0.83[ASN][1000 genomes]
rs59389433	0.83[ASN][1000 genomes]
rs59691280	0.83[ASN][1000 genomes]
rs6492991	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6492992	0.82[ASN][1000 genomes]
rs6492993	1.00[ASW][hapmap];0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6492994	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492998	0.85[TSI][hapmap]
rs690733	0.84[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes]
rs691702	0.83[EUR][1000 genomes]
rs692153	0.82[CHD][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs7162443	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7162503	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166205	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7166905	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7167813	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170049	0.89[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs7173086	0.92[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7175912	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178840	0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7179231	0.83[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7179969	0.83[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs8026858	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs8032589	0.80[JPT][hapmap]
rs8035252	0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs8036602	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8038834	0.83[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs8039014	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs8039915	0.83[ASN][1000 genomes]
rs8039934	0.83[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs8043253	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs909023	0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs909024	0.85[ASN][1000 genomes]
rs909025	0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9972349	0.89[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9972622	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9972623	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457120	chr15:41410705-41546631	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv569231	chr15:41410705-41546631	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv1844058	chr15:41511916-41548948	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv1045455	chr15:41536624-41620534	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6492997	NDUFAF1	cis	cerebellum	SCAN
rs6492997	NDUFAF1	cis	parietal	SCAN
rs6492997	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs6492997	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs6492997	BUB1B	cis	parietal	SCAN
rs6492997	NDUFAF1	cis	Muscle Skeletal	GTEx
rs6492997	GPR176	cis	parietal	SCAN
rs6492997	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs6492997	TTBK2	cis	cerebellum	SCAN
rs6492997	NUSAP1	cis	cerebellum	SCAN
rs6492997	NDUFAF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41524200-41546200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:41524200-41554800	Weak transcription	Fetal Thymus	thymus
3	chr15:41524200-41555800	Weak transcription	Aorta	Aorta
4	chr15:41524200-41563800	Weak transcription	Small Intestine	intestine
5	chr15:41524200-41575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:41524400-41555800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:41524800-41546200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:41524800-41563800	Weak transcription	Esophagus	oesophagus
9	chr15:41525000-41548400	Weak transcription	Fetal Lung	lung
10	chr15:41525200-41548200	Weak transcription	Fetal Kidney	kidney
11	chr15:41525200-41554200	Weak transcription	Fetal Brain Female	brain
12	chr15:41525200-41556400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:41525200-41575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:41525400-41556200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr15:41525400-41556800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr15:41525800-41554800	Weak transcription	Dnd41	blood
17	chr15:41525800-41575200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:41526000-41541800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:41526000-41554800	Weak transcription	Brain Angular Gyrus	brain
20	chr15:41526200-41542200	Weak transcription	NH-A	brain
21	chr15:41526200-41554800	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:41526400-41542200	Weak transcription	HSMMtube	muscle
23	chr15:41532000-41542000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:41532400-41550600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr15:41533200-41548400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:41533200-41552400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:41533800-41554600	Weak transcription	Brain Anterior Caudate	brain
28	chr15:41533800-41555000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:41534000-41541200	Weak transcription	Thymus	Thymus
30	chr15:41534000-41542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:41534000-41543200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:41534000-41555200	Weak transcription	Brain Germinal Matrix	brain
33	chr15:41534200-41551000	Weak transcription	GM12878-XiMat	blood
34	chr15:41534200-41555200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:41534200-41556400	Weak transcription	Spleen	Spleen
36	chr15:41534400-41544600	Weak transcription	HSMM	muscle
37	chr15:41535400-41541600	Strong transcription	Fetal Stomach	stomach
38	chr15:41535600-41541400	Strong transcription	Liver	Liver
39	chr15:41535600-41541600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:41535600-41542200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:41535800-41541200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:41535800-41541600	Strong transcription	Placenta	Placenta
43	chr15:41536000-41542600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:41536600-41573600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr15:41536800-41555000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr15:41536800-41555200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:41537000-41546400	Weak transcription	K562	blood
48	chr15:41537000-41549800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:41537200-41541400	Weak transcription	HepG2	liver
50	chr15:41537200-41542000	Weak transcription	NHLF	lung

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