Variant report

Variant	rs2578539
Chromosome Location	chr5:5494739-5494740
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:2060401..2061330-chr5:5494671..5495442,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1115068	0.80[CEU][hapmap]
rs1541799	0.85[GIH][hapmap];0.80[TSI][hapmap]
rs252940	0.84[EUR][1000 genomes]
rs2578500	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs2578552	0.85[GIH][hapmap];0.82[TSI][hapmap]
rs2578565	0.81[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs2918261	1.00[CHB][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap]
rs2964159	0.87[GIH][hapmap]
rs3097160	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6894118	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv528961	chr5:5494739-5496480	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2578539	NDUFS6	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5433400-5495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:5458600-5495000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:5465200-5495000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:5475400-5495000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:5477200-5497600	Weak transcription	Brain Angular Gyrus	brain
6	chr5:5482200-5495000	Weak transcription	NHEK	skin
7	chr5:5482800-5497600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:5487400-5495000	Weak transcription	Gastric	stomach
9	chr5:5490200-5495000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:5490200-5495000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:5490600-5497200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:5490600-5497600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:5490800-5496400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:5491400-5495000	Weak transcription	Lung	lung
15	chr5:5491400-5496400	Weak transcription	Hela-S3	cervix
16	chr5:5492200-5495400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr5:5492800-5497400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:5493600-5495600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:5493800-5494800	Enhancers	NHDF-Ad	bronchial
20	chr5:5493800-5495200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:5493800-5495400	Enhancers	Fetal Heart	heart
22	chr5:5493800-5495400	Bivalent Enhancer	Fetal Stomach	stomach
23	chr5:5493800-5495800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:5494000-5494800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
25	chr5:5494000-5494800	Enhancers	HMEC	breast
26	chr5:5494000-5495000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr5:5494000-5495000	Enhancers	Fetal Intestine Small	intestine
28	chr5:5494000-5495200	Enhancers	Primary T cells from cord blood	blood
29	chr5:5494000-5495200	Enhancers	Placenta	Placenta
30	chr5:5494000-5495400	Enhancers	Primary hematopoietic stem cells	blood
31	chr5:5494000-5495400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
32	chr5:5494000-5495400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:5494000-5495400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr5:5494000-5495400	Enhancers	Esophagus	oesophagus
35	chr5:5494000-5495400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr5:5494000-5495400	Enhancers	Fetal Brain Male	brain
37	chr5:5494000-5495400	Enhancers	Spleen	Spleen
38	chr5:5494000-5495600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:5494000-5495600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr5:5494000-5495600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:5494000-5496200	Enhancers	Psoas Muscle	Psoas
42	chr5:5494000-5496400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:5494200-5495000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr5:5494200-5495000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:5494200-5495000	Enhancers	Adipose Nuclei	Adipose
46	chr5:5494200-5495000	Enhancers	Brain Germinal Matrix	brain
47	chr5:5494200-5495200	Enhancers	Stomach Mucosa	stomach
48	chr5:5494200-5495400	Enhancers	K562	blood
49	chr5:5494400-5494800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:5494400-5494800	Flanking Active TSS	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links