Variant report

Variant	rs171801
Chromosome Location	chr5:58711828-58711829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58709583..58712076-chr5:58713537..58715588,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs165940	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs16889733	0.84[ASN][1000 genomes]
rs171800	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs181736	0.83[CHB][hapmap]
rs187368	0.86[ASN][1000 genomes]
rs187716	0.92[ASN][1000 genomes]
rs244566	0.82[ASN][1000 genomes]
rs244568	0.86[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs244569	0.83[ASN][1000 genomes]
rs244591	0.90[JPT][hapmap]
rs244592	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs244593	0.82[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs244594	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs244595	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs244596	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs244597	0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs258104	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs258105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs258106	0.83[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs258108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs258109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs258110	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs258111	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs258127	0.86[JPT][hapmap];0.82[MEX][hapmap]
rs258128	0.86[JPT][hapmap]
rs258129	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2591750	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs2607343	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs371775	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs378858	0.86[JPT][hapmap]
rs378869	0.83[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs378970	0.86[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs380118	0.88[ASN][1000 genomes]
rs380993	0.86[JPT][hapmap]
rs381755	0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs383444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs387647	0.85[JPT][hapmap]
rs392901	0.89[JPT][hapmap]
rs401013	0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs403672	0.86[JPT][hapmap]
rs403695	0.86[JPT][hapmap]
rs419744	0.85[ASN][1000 genomes]
rs419953	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs424839	0.86[JPT][hapmap]
rs427433	0.86[ASN][1000 genomes]
rs427740	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs427748	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs428059	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs429191	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs433161	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs433565	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs434183	0.86[ASN][1000 genomes]
rs434422	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs441817	0.86[ASN][1000 genomes]
rs443191	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs444552	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs454702	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs487029	0.81[ASN][1000 genomes]
rs573230	0.86[ASN][1000 genomes]
rs573336	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs575045	0.88[ASN][1000 genomes]
rs62355534	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62355535	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62355536	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs651576	0.81[ASN][1000 genomes]
rs669240	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs670169	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv881705	chr5:58668669-58745872	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1034656	chr5:58674724-58755580	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv598253	chr5:58675538-58754510	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs171801	NDUFAF2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58704200-58714200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:58704600-58712000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:58704600-58712200	Weak transcription	Fetal Lung	lung
4	chr5:58705600-58751400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:58707600-58714800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:58708400-58712200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:58708600-58718200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:58709800-58712200	Genic enhancers	A549	lung
9	chr5:58709800-58756800	Weak transcription	Aorta	Aorta
10	chr5:58710200-58713000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr5:58710400-58714200	Weak transcription	Fetal Intestine Large	intestine
12	chr5:58710800-58714400	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:58711000-58713400	Weak transcription	Small Intestine	intestine
14	chr5:58711200-58713400	Weak transcription	Fetal Intestine Small	intestine
15	chr5:58711800-58712200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:58711800-58712200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:58711800-58712400	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links