Variant report

Variant	rs16969559
Chromosome Location	chr15:39974216-39974217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39881447..39883464-chr15:39972745..39975261,2	MCF-7	breast:
2	chr15:39974204..39976528-chr15:39982397..39984405,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10520139	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1551946	1.00[CHD][hapmap]
rs16969468	1.00[ASN][1000 genomes]
rs16969544	1.00[ASN][1000 genomes]
rs16969546	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs16969550	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16969551	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs16969552	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16969553	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16969554	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16969556	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16969558	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969560	1.00[ASW][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16969563	1.00[ASN][1000 genomes]
rs2411302	0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57588844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58098811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58813139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61614874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6492905	1.00[CHD][hapmap]
rs7168558	1.00[ASN][1000 genomes]
rs7171103	1.00[ASN][1000 genomes]
rs7179020	1.00[ASN][1000 genomes]
rs7183539	0.83[LWK][hapmap];0.81[MKK][hapmap]
rs73393229	1.00[ASN][1000 genomes]
rs73393230	1.00[ASN][1000 genomes]
rs73393232	1.00[ASN][1000 genomes]
rs7494926	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7498087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8024038	1.00[CHD][hapmap]
rs8028707	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	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
6	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:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39972600-39975000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr15:39972600-39975400	Enhancers	Rectal Smooth Muscle	rectum
3	chr15:39972600-39975400	Enhancers	Osteobl	bone
4	chr15:39972600-39975600	Enhancers	HSMMtube	muscle
5	chr15:39972600-39976400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:39972600-39978800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:39972800-39977000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr15:39973000-39975400	Enhancers	NHDF-Ad	bronchial
9	chr15:39973200-39975400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:39973200-39975600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:39973400-39974600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:39973400-39982800	Weak transcription	Fetal Lung	lung
13	chr15:39973800-39982800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:39974000-39974600	Enhancers	Colon Smooth Muscle	Colon
15	chr15:39974000-39974800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:39974000-39975000	Enhancers	HSMM	muscle
17	chr15:39974000-39975400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr15:39974200-39975400	Enhancers	Fetal Kidney	kidney
19	chr15:39974200-39978400	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links