Variant report

Variant	rs294492
Chromosome Location	chr5:58860127-58860128
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:58853948..58856765-chr5:58857609..58860199,2	MCF-7	breast:
2	chr5:58858064..58860308-chr5:58864549..58867326,2	K562	blood:
3	chr5:58843792..58846510-chr5:58858792..58861752,2	MCF-7	breast:
4	chr5:58853827..58855352-chr5:58858550..58860453,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10805516	0.86[CEU][hapmap];0.84[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs159194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs159196	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs159197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs177077	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs177078	0.83[ASN][1000 genomes]
rs186078	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs190936	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs294477	0.95[ASN][1000 genomes]
rs294478	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs294479	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs294481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs294482	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs294483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs294484	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs294485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs294486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs294494	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294495	0.95[ASN][1000 genomes]
rs294496	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs294497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs294498	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs294499	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs294500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs294501	0.97[ASN][1000 genomes]
rs294502	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295943	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs295944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295946	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs295948	0.93[ASN][1000 genomes]
rs295950	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295951	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295952	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs295953	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295954	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295955	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295956	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295957	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295958	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs295960	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs295962	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295963	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[TSI][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295964	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295965	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295966	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295967	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295968	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295969	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295970	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295971	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295972	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295974	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295975	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295978	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295979	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs295980	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298014	0.87[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298016	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs298017	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs298025	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298027	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298028	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298029	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298030	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298032	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298033	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298034	0.87[ASW][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs298036	0.83[ASN][1000 genomes]
rs298038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs298039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs298040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs298041	0.83[ASN][1000 genomes]
rs298043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs298044	0.87[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs298045	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs298046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs298047	0.83[ASN][1000 genomes]
rs298048	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs298051	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs298052	0.87[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs298053	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs37570	0.96[ASN][1000 genomes]
rs37571	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462189	chr5:58830145-58879822	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598255	chr5:58830145-58879822	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs294492	NDUFAF2	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58843800-58862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:58850400-58860800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:58854600-58861600	Weak transcription	Fetal Brain Female	brain
4	chr5:58855600-58863000	Enhancers	Primary B cells from peripheral blood	blood
5	chr5:58856600-58864000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:58856600-58865400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:58857800-58860200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:58857800-58860400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:58858200-58860200	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr5:58858200-58860400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:58858600-58860200	Enhancers	HUVEC	blood vessel
12	chr5:58858600-58861400	Enhancers	Stomach Mucosa	stomach
13	chr5:58858600-58862600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr5:58858800-58860200	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr5:58858800-58861600	Enhancers	Thymus	Thymus
16	chr5:58859000-58860200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr5:58859000-58860400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr5:58859000-58860600	Weak transcription	Gastric	stomach
19	chr5:58859200-58860200	Enhancers	GM12878-XiMat	blood
20	chr5:58859200-58860800	Weak transcription	Fetal Intestine Small	intestine
21	chr5:58859200-58861200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:58859200-58883400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:58859400-58860600	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:58859400-58865200	Weak transcription	Brain Substantia Nigra	brain
25	chr5:58859400-58870400	Weak transcription	Fetal Intestine Large	intestine
26	chr5:58859400-58871600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:58859400-58884000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:58859600-58860600	Enhancers	Primary B cells from cord blood	blood
29	chr5:58859600-58860600	Genic enhancers	A549	lung
30	chr5:58859600-58862600	Enhancers	Hela-S3	cervix
31	chr5:58859600-58864800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:58859800-58860600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:58859800-58860600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:58859800-58860600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:58859800-58860800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:58859800-58861800	Enhancers	Psoas Muscle	Psoas
37	chr5:58859800-58863200	Weak transcription	Fetal Lung	lung
38	chr5:58859800-58864400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:58859800-58865400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr5:58859800-58873800	Weak transcription	HSMM	muscle
41	chr5:58860000-58860400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:58860000-58860400	Weak transcription	HMEC	breast
43	chr5:58860000-58866200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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