Variant report

Variant	rs252938
Chromosome Location	chr5:5496480-5496481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10063885	0.91[CEU][hapmap]
rs252928	0.86[EUR][1000 genomes]
rs252929	0.83[EUR][1000 genomes]
rs252930	0.84[EUR][1000 genomes]
rs252934	0.80[EUR][1000 genomes]
rs252937	0.84[ASN][1000 genomes]
rs2560299	0.87[CEU][hapmap]
rs2560300	0.87[CEU][hapmap]
rs2578513	0.83[EUR][1000 genomes]
rs2578514	0.83[EUR][1000 genomes]
rs2578515	0.83[EUR][1000 genomes]
rs2578516	0.83[EUR][1000 genomes]
rs2578527	0.82[EUR][1000 genomes]
rs2578553	0.87[CEU][hapmap]
rs2578554	0.91[CEU][hapmap]
rs2578557	0.87[CEU][hapmap]
rs2578564	0.91[CEU][hapmap]
rs2591694	0.82[EUR][1000 genomes]
rs2591696	0.81[EUR][1000 genomes]
rs2591697	0.83[EUR][1000 genomes]
rs2619829	0.82[EUR][1000 genomes]
rs2619855	0.88[EUR][1000 genomes]
rs2652705	0.82[EUR][1000 genomes]
rs2652707	0.81[EUR][1000 genomes]
rs2652715	0.85[EUR][1000 genomes]
rs2918260	0.91[CEU][hapmap]
rs2928223	0.84[EUR][1000 genomes]
rs2928225	0.87[EUR][1000 genomes]
rs3098377	0.91[CEU][hapmap]
rs719080	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
4	esv3411514	chr5:5495732-5497984	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1008476	chr5:5495880-5497926	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3471522	chr5:5495931-5497962	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3471523	chr5:5495931-5497962	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv995745	chr5:5496080-5497822	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv518861	chr5:5496203-5496480	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs252938	NDUFS6	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5477200-5497600	Weak transcription	Brain Angular Gyrus	brain
2	chr5:5482800-5497600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:5490600-5497200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:5490600-5497600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:5492800-5497400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:5494800-5497200	Weak transcription	HMEC	breast
7	chr5:5494800-5503800	Weak transcription	GM12878-XiMat	blood
8	chr5:5495200-5497000	Weak transcription	Colon Smooth Muscle	Colon
9	chr5:5495200-5497200	Weak transcription	Brain Anterior Caudate	brain
10	chr5:5495200-5498400	Enhancers	Brain Germinal Matrix	brain
11	chr5:5495400-5496600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:5495400-5496600	Weak transcription	Fetal Brain Male	brain
13	chr5:5495400-5496800	Enhancers	Adipose Nuclei	Adipose
14	chr5:5495400-5497000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr5:5495400-5497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:5495400-5497200	Weak transcription	Liver	Liver
17	chr5:5495400-5497200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr5:5495400-5497200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:5495400-5497600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:5495400-5497600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr5:5495400-5497800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:5495600-5497200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:5495600-5497200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:5495800-5496800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:5495800-5497000	Enhancers	Brain Hippocampus Middle	brain
26	chr5:5496000-5496600	Enhancers	Gastric	stomach
27	chr5:5496000-5496800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:5496000-5497200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:5496000-5497600	Enhancers	Brain Cingulate Gyrus	brain
30	chr5:5496200-5497600	Enhancers	Brain Substantia Nigra	brain
31	chr5:5496200-5497600	Weak transcription	Psoas Muscle	Psoas
32	chr5:5496400-5496600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
33	chr5:5496400-5496600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
34	chr5:5496400-5496600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
35	chr5:5496400-5497200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
36	chr5:5496400-5497800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr5:5496400-5498000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:5496400-5498000	Enhancers	Fetal Brain Female	brain

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