Variant report

Variant	rs426659
Chromosome Location	chr5:53319404-53319405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:53318073..53320029-chr5:53321875..53324645,4	K562	blood:
2	chr5:53313684..53316235-chr5:53319092..53322821,4	K562	blood:
3	chr5:53317383..53319420-chr5:53606124..53608735,2	K562	blood:
4	chr5:53310230..53312789-chr5:53319399..53321683,2	K562	blood:
5	chr5:53317328..53319798-chr5:53320168..53323539,4	K562	blood:

Variant related genes	Relation type
ENSG00000185305	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13180378	0.81[CHB][hapmap]
rs156836	0.81[CHB][hapmap]
rs194281	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs255747	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs255748	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs255749	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255750	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs255751	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255754	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255758	0.81[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs255760	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs273223	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs274362	1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs31127	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs31226	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs373284	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs406517	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6874203	0.81[CHB][hapmap]
rs696007	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs697109	0.81[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv830299	chr5:53207020-53386600	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv881265	chr5:53305742-53504764	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
9	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
12	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
13	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
14	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
15	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
16	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
17	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
18	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs426659	NDUFS4	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53310600-53336000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:53314600-53321800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:53316200-53335200	Weak transcription	Gastric	stomach
4	chr5:53316200-53387400	Weak transcription	Left Ventricle	heart
5	chr5:53316400-53319600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:53316400-53324000	Weak transcription	Primary B cells from cord blood	blood
7	chr5:53317600-53319800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:53318000-53319600	Enhancers	Fetal Intestine Large	intestine
9	chr5:53318000-53337200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:53318200-53319600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:53318200-53319800	Enhancers	K562	blood
12	chr5:53318200-53319800	Weak transcription	NHDF-Ad	bronchial
13	chr5:53318200-53319800	Weak transcription	Osteobl	bone
14	chr5:53318200-53320000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:53318200-53320000	Weak transcription	NHEK	skin
16	chr5:53318200-53329200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:53318400-53319800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr5:53318400-53319800	Weak transcription	HMEC	breast
19	chr5:53318400-53319800	Weak transcription	NHLF	lung
20	chr5:53318400-53320200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:53318400-53320400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:53318400-53321000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:53318600-53319600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:53318600-53319600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:53318600-53319600	Weak transcription	Fetal Intestine Small	intestine
26	chr5:53318600-53322200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:53318800-53320000	Enhancers	Dnd41	blood
28	chr5:53318800-53320400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:53318800-53320800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:53318800-53326400	Weak transcription	Primary T cells from cord blood	blood
31	chr5:53318800-53330400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr5:53319000-53319600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr5:53319000-53319600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr5:53319400-53321600	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links