Variant report

Variant	rs6879987
Chromosome Location	chr5:124572770-124572771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10045892	0.84[EUR][1000 genomes]
rs11241796	0.94[EUR][1000 genomes]
rs11241797	0.93[EUR][1000 genomes]
rs11959358	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1347923	0.94[EUR][1000 genomes]
rs1347925	0.94[EUR][1000 genomes]
rs1348584	0.94[EUR][1000 genomes]
rs1439582	0.88[EUR][1000 genomes]
rs1439583	0.89[EUR][1000 genomes]
rs1439586	0.92[EUR][1000 genomes]
rs1439611	0.94[EUR][1000 genomes]
rs1444659	0.94[EUR][1000 genomes]
rs2118999	0.84[EUR][1000 genomes]
rs4351146	0.94[EUR][1000 genomes]
rs5011755	0.92[EUR][1000 genomes]
rs6595604	0.92[EUR][1000 genomes]
rs6595606	0.81[EUR][1000 genomes]
rs713163	0.94[EUR][1000 genomes]
rs7731555	0.93[EUR][1000 genomes]
rs7737255	0.91[EUR][1000 genomes]
rs996377	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882823	chr5:124569471-124639468	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6879987	SRFBP1	cis	cerebellum	SCAN
rs6879987	CTXN3	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124546600-124585200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:124568600-124573400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:124571200-124573200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr5:124571200-124573400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:124571200-124573600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr5:124571200-124573600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:124571400-124573000	Enhancers	Fetal Heart	heart
8	chr5:124571400-124573400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:124571400-124573400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr5:124571400-124573600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:124571600-124572800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:124571600-124573000	Enhancers	Fetal Brain Male	brain
13	chr5:124571600-124573200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr5:124571600-124573200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr5:124571600-124573200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:124571600-124573200	Enhancers	Brain Anterior Caudate	brain
17	chr5:124571600-124573200	Enhancers	Fetal Brain Female	brain
18	chr5:124571800-124572800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:124571800-124573200	Enhancers	H9 Cell Line	embryonic stem cell
20	chr5:124571800-124573200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:124572000-124572800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr5:124572000-124572800	Weak transcription	Left Ventricle	heart
23	chr5:124572000-124573200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr5:124572400-124573200	Enhancers	Brain Hippocampus Middle	brain
25	chr5:124572400-124573200	Enhancers	Brain Substantia Nigra	brain
26	chr5:124572600-124573000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr5:124572600-124573000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:124572600-124573000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:124572600-124573000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr5:124572600-124573200	Enhancers	Brain Angular Gyrus	brain
31	chr5:124572600-124573400	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links