Variant report

Variant	rs2578565
Chromosome Location	chr5:5460569-5460570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1004263	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10063885	0.83[EUR][1000 genomes]
rs1115068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12653733	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541799	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2560297	0.87[EUR][1000 genomes]
rs2560298	0.86[EUR][1000 genomes]
rs2560299	0.85[EUR][1000 genomes]
rs2560300	0.85[EUR][1000 genomes]
rs2578500	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2578501	0.90[EUR][1000 genomes]
rs2578548	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2578549	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2578550	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2578552	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2578553	0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs2578554	0.85[EUR][1000 genomes]
rs2578556	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2578557	0.86[EUR][1000 genomes]
rs2578558	0.82[EUR][1000 genomes]
rs2578559	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2578564	0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs2619827	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2619844	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918253	0.84[EUR][1000 genomes]
rs2918260	0.86[EUR][1000 genomes]
rs2918261	0.95[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2964131	0.83[EUR][1000 genomes]
rs2964155	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964159	0.85[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2964160	0.86[EUR][1000 genomes]
rs3097160	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3098377	0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs61063822	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6894118	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757981	chr5:5447098-5764620	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv2759319	chr5:5447098-5764620	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2578565	NDUFS6	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5430200-5478800	Weak transcription	Stomach Mucosa	stomach
2	chr5:5430800-5460800	Weak transcription	Fetal Heart	heart
3	chr5:5433400-5495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:5436600-5468400	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr5:5436600-5470600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:5436600-5471400	Strong transcription	Hela-S3	cervix
7	chr5:5436600-5478200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:5436800-5470400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:5436800-5470600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr5:5437200-5470600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:5437200-5477000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr5:5437400-5470800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:5437400-5480000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:5437600-5470600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:5437800-5470600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:5439600-5470600	Strong transcription	Dnd41	blood
17	chr5:5440000-5470600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr5:5440800-5471600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:5441200-5468800	Strong transcription	Liver	Liver
20	chr5:5441400-5468400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:5441400-5468800	Strong transcription	Adipose Nuclei	Adipose
22	chr5:5441400-5469000	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:5441400-5470400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:5441600-5465200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr5:5441600-5468800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:5441600-5469000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr5:5441600-5470600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr5:5442400-5475800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr5:5446800-5467000	Strong transcription	NH-A	brain
30	chr5:5448800-5470400	Strong transcription	Primary B cells from cord blood	blood
31	chr5:5449800-5461000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:5451800-5467400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr5:5452600-5468400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:5452600-5472000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:5452800-5464000	Strong transcription	HUVEC	blood vessel
36	chr5:5453000-5464800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:5453000-5467600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:5453000-5467600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:5453200-5463200	Strong transcription	Colon Smooth Muscle	Colon
40	chr5:5453200-5465200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:5453200-5468400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:5453200-5468400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:5453200-5468400	Strong transcription	Fetal Muscle Leg	muscle
44	chr5:5453200-5470400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr5:5453400-5462800	Strong transcription	K562	blood
46	chr5:5453400-5463400	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr5:5453400-5468400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr5:5453400-5469200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:5453800-5470600	Strong transcription	Primary T cells from cord blood	blood
50	chr5:5454000-5463800	Strong transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links