Variant report

Variant	rs2963419
Chromosome Location	chr5:8840433-8840434
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEMA5A-1	chr5:8839666-8840502	XLOC_004729

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13164632	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904938	0.91[ASN][1000 genomes]
rs2963319	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963320	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963407	0.86[EUR][1000 genomes]
rs2963410	0.86[EUR][1000 genomes]
rs2963415	0.86[EUR][1000 genomes]
rs2963416	0.86[EUR][1000 genomes]
rs2963418	0.86[EUR][1000 genomes]
rs4266375	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	esv3492014	chr5:8749469-9004066	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3492015	chr5:8749469-9004066	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
8	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 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	chr5:8827400-8843800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:8829800-8843000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:8830400-8842600	Weak transcription	NHLF	lung
4	chr5:8836200-8840600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:8839400-8840800	Active TSS	Brain Angular Gyrus	brain
6	chr5:8839600-8840800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:8839800-8840800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:8839800-8843000	Weak transcription	NH-A	brain
9	chr5:8839800-8843600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:8840000-8840600	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr5:8840000-8840600	Flanking Active TSS	Brain Substantia Nigra	brain
12	chr5:8840000-8843200	Weak transcription	Osteobl	bone
13	chr5:8840000-8844000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:8840000-8844000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:8840200-8840600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr5:8840200-8840800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr5:8840200-8840800	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr5:8840200-8840800	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr5:8840200-8841000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:8840200-8842200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:8840200-8843200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:8840400-8841000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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