Variant report

Variant	rs16969030
Chromosome Location	chr15:39740238-39740239
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39739352..39742846-chr15:39745277..39748876,4	MCF-7	breast:
2	chr15:39739658..39743220-chr15:39872774..39876303,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16952148	1.00[AMR][1000 genomes]
rs16969021	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969032	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969052	1.00[AMR][1000 genomes]
rs16969077	1.00[AMR][1000 genomes]
rs16969097	1.00[AMR][1000 genomes]
rs16969108	1.00[AMR][1000 genomes]
rs16969113	1.00[AMR][1000 genomes]
rs4091683	1.00[AMR][1000 genomes]
rs60614142	1.00[AMR][1000 genomes]
rs60827388	1.00[AMR][1000 genomes]
rs73385063	1.00[AMR][1000 genomes]
rs74010137	1.00[AMR][1000 genomes]
rs8030678	1.00[AMR][1000 genomes]
rs9672485	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	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

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39727200-39746800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr15:39737200-39742800	Weak transcription	Lung	lung
3	chr15:39737400-39742400	Weak transcription	Fetal Stomach	stomach
4	chr15:39737600-39742400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:39737800-39742600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:39738600-39741000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:39739000-39741200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:39739200-39740400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:39739200-39740400	Weak transcription	Fetal Thymus	thymus
10	chr15:39739400-39740800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr15:39739400-39742400	Enhancers	HepG2	liver
12	chr15:39739600-39740400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:39739600-39740400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr15:39740000-39740400	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr15:39740000-39740400	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr15:39740000-39759400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:39740200-39740800	Enhancers	Fetal Muscle Leg	muscle
18	chr15:39740200-39740800	Enhancers	GM12878-XiMat	blood
19	chr15:39740200-39741000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:39740200-39741200	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links