Variant report

Variant	rs17254450
Chromosome Location	chr14:21325687-21325688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:21307828..21309542-chr14:21323768..21326232,2	MCF-7	breast:
2	chr14:21325535..21326543-chr14:21438744..21440024,15	MCF-7	breast:
3	chr14:21165586..21166230-chr14:21325546..21326484,3	MCF-7	breast:
4	chr14:21325086..21326530-chr14:21507784..21508853,5	MCF-7	breast:
5	chr14:21325127..21326043-chr14:21559445..21560171,2	MCF-7	breast:
6	chr14:21165736..21166589-chr14:21325539..21326522,2	K562	blood:
7	chr14:21325525..21326443-chr14:21341560..21342549,4	MCF-7	breast:
8	chr14:21325658..21326220-chr14:21473825..21474579,2	MCF-7	breast:
9	chr14:21164738..21167054-chr14:21324271..21326741,2	MCF-7	breast:
10	chr14:21306953..21309140-chr14:21323464..21326358,2	K562	blood:
11	chr14:21325580..21326139-chr14:21341851..21342353,2	MCF-7	breast:
12	chr14:21325537..21326206-chr14:21438780..21439731,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259130	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10139443	0.83[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs10140301	0.87[ASN][1000 genomes]
rs10144045	0.88[ASN][1000 genomes]
rs10162308	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10872858	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11156730	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11623919	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11845945	0.82[ASN][1000 genomes]
rs12878116	0.87[ASN][1000 genomes]
rs17182206	0.94[ASN][1000 genomes]
rs17182243	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17254436	0.94[ASN][1000 genomes]
rs17254457	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1889771	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1889772	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28398970	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28522687	0.94[ASN][1000 genomes]
rs61978607	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68014001	0.98[ASN][1000 genomes]
rs8011501	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8014985	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8016193	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs8020174	0.94[ASN][1000 genomes]
rs983671	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv1045505	chr14:21168839-21337972	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2758349	chr14:21216108-21471614	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv2759972	chr14:21216108-21471614	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv427936	chr14:21216108-21531783	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
7	nsv428293	chr14:21216108-21531783	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21317200-21325800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr14:21317400-21326000	Weak transcription	Fetal Intestine Small	intestine
3	chr14:21317800-21325800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:21324000-21325800	Weak transcription	Liver	Liver
5	chr14:21324000-21325800	Weak transcription	Brain Angular Gyrus	brain
6	chr14:21324000-21325800	Weak transcription	Brain Anterior Caudate	brain
7	chr14:21324000-21325800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr14:21324000-21325800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr14:21324000-21325800	Weak transcription	Brain Substantia Nigra	brain
10	chr14:21324000-21325800	Weak transcription	Fetal Intestine Large	intestine
11	chr14:21324000-21325800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr14:21324000-21326000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr14:21324000-21326000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr14:21324400-21325800	Weak transcription	Brain Hippocampus Middle	brain
15	chr14:21324400-21325800	Weak transcription	A549	lung
16	chr14:21324400-21326200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr14:21325600-21325800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr14:21325600-21325800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr14:21325600-21325800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr14:21325600-21325800	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr14:21325600-21325800	Enhancers	Stomach Mucosa	stomach
22	chr14:21325600-21326000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr14:21325600-21326000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr14:21325600-21326000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr14:21325600-21326000	Bivalent Enhancer	Dnd41	blood
26	chr14:21325600-21326000	Enhancers	GM12878-XiMat	blood
27	chr14:21325600-21326200	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links