Variant report

Variant	rs16969563
Chromosome Location	chr15:39977297-39977298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39879533..39881128-chr15:39975849..39978589,2	MCF-7	breast:
2	chr15:39970946..39972783-chr15:39976186..39977886,2	MCF-7	breast:
3	chr15:39977207..39979159-chr15:39990602..39992278,2	K562	blood:
4	chr15:39976358..39978991-chr15:39987825..39990232,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-THBS1-3	chr15:39976380-39977579	l_1149_chr15:39975419-39977579_lung

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10520139	1.00[ASN][1000 genomes]
rs10520140	1.00[AMR][1000 genomes]
rs12911910	0.89[YRI][hapmap]
rs16969468	1.00[ASN][1000 genomes]
rs16969527	0.90[YRI][hapmap]
rs16969537	0.89[YRI][hapmap]
rs16969544	1.00[ASN][1000 genomes]
rs16969546	1.00[ASN][1000 genomes]
rs16969550	1.00[ASN][1000 genomes]
rs16969552	1.00[ASN][1000 genomes]
rs16969553	1.00[ASN][1000 genomes]
rs16969554	1.00[ASN][1000 genomes]
rs16969556	1.00[ASN][1000 genomes]
rs16969559	1.00[ASN][1000 genomes]
rs16969560	1.00[ASN][1000 genomes]
rs4641712	0.90[YRI][hapmap]
rs56715321	1.00[AMR][1000 genomes]
rs57588844	1.00[ASN][1000 genomes]
rs58098811	1.00[ASN][1000 genomes]
rs58813139	1.00[ASN][1000 genomes]
rs61614874	1.00[ASN][1000 genomes]
rs7168558	1.00[ASN][1000 genomes]
rs7171103	1.00[ASN][1000 genomes]
rs7179020	1.00[ASN][1000 genomes]
rs73393229	1.00[ASN][1000 genomes]
rs73393230	1.00[ASN][1000 genomes]
rs73393232	1.00[ASN][1000 genomes]
rs7494926	1.00[ASN][1000 genomes]
rs7498087	1.00[ASN][1000 genomes]
rs8028707	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39972600-39978800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:39973400-39982800	Weak transcription	Fetal Lung	lung
3	chr15:39973800-39982800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:39974200-39978400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:39974800-39985000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:39975000-39978000	Weak transcription	HSMM	muscle
7	chr15:39975000-39978600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:39975400-39982000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:39975400-39984400	Weak transcription	Fetal Kidney	kidney
10	chr15:39975600-39978000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:39976800-39978000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:39976800-39978400	Enhancers	Osteobl	bone
13	chr15:39976800-39978800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:39977000-39978200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:39977000-39978200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:39977000-39978400	Enhancers	HSMMtube	muscle
17	chr15:39977200-39990600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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