Variant report

Variant	rs11619239
Chromosome Location	chr13:53479775-53479776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11619880	0.89[ASN][1000 genomes]
rs1980691	0.93[ASN][1000 genomes]
rs61950422	0.87[ASN][1000 genomes]
rs61950423	0.89[ASN][1000 genomes]
rs61950424	0.89[ASN][1000 genomes]
rs61950443	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7986215	0.87[ASN][1000 genomes]

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	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv900090	chr13:53429453-53495715	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11619239	CAB39L	cis	cerebellum	SCAN
rs11619239	LOC220429	cis	cerebellum	SCAN
rs11619239	NEK3	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53476000-53482200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr13:53476200-53480200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr13:53476200-53481000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:53476200-53482400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr13:53476400-53482000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr13:53476600-53480600	Enhancers	Brain Germinal Matrix	brain
7	chr13:53476600-53481200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr13:53476600-53482400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:53476800-53482000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr13:53477000-53481000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr13:53477200-53480600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr13:53477600-53480400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr13:53477600-53480600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr13:53478400-53480600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:53478400-53480800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr13:53479000-53479800	Enhancers	Brain Anterior Caudate	brain
17	chr13:53479000-53479800	Enhancers	Brain Substantia Nigra	brain
18	chr13:53479200-53480000	Enhancers	Brain Hippocampus Middle	brain
19	chr13:53479200-53480400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr13:53479200-53480400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr13:53479200-53480800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr13:53479400-53481200	Enhancers	Fetal Brain Female	brain
23	chr13:53479400-53482000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr13:53479400-53482200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr13:53479600-53479800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
26	chr13:53479600-53479800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:53479600-53480000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:53479600-53480000	Bivalent Enhancer	Fetal Kidney	kidney
29	chr13:53479600-53480600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links