Variant report

Variant	rs9939344
Chromosome Location	chr16:47892624-47892625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHKB-2	chr16:47892490-47893840	ENSG00000261231.2

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13336450	0.99[AFR][1000 genomes]
rs1985323	0.86[YRI][hapmap]
rs28415596	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28421488	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6500353	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6500354	0.83[AFR][1000 genomes]
rs7202593	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7205450	0.81[AFR][1000 genomes]
rs8045787	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8045788	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8045934	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8048023	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8048189	0.81[AFR][1000 genomes]
rs8054600	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9921499	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926879	1.00[YRI][hapmap]
rs9929891	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9931056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9935449	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520355	chr16:47424828-48164777	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv525976	chr16:47583872-48035026	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428657	chr16:47748036-47913816	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv833218	chr16:47869819-48051745	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47883400-47899600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr16:47883800-47893000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr16:47889400-47893400	Enhancers	Brain Germinal Matrix	brain
4	chr16:47890600-47893400	Enhancers	Fetal Brain Female	brain
5	chr16:47891600-47893400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr16:47891600-47893400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr16:47891600-47893800	Enhancers	Fetal Brain Male	brain
8	chr16:47892000-47892800	Enhancers	A549	lung
9	chr16:47892000-47893400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr16:47892200-47892800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr16:47892200-47893200	Enhancers	Brain Hippocampus Middle	brain
12	chr16:47892200-47893200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr16:47892200-47893200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr16:47892200-47893400	Enhancers	HMEC	breast
15	chr16:47892200-47893400	Enhancers	NHEK	skin
16	chr16:47892400-47892800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:47892400-47893000	Bivalent Enhancer	NH-A	brain
18	chr16:47892400-47893400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:47892600-47892800	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr16:47892600-47892800	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr16:47892600-47893200	Enhancers	Brain Angular Gyrus	brain
22	chr16:47892600-47893200	Enhancers	Fetal Stomach	stomach

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