Variant report

Variant	rs9963959
Chromosome Location	chr18:29146950-29146951
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29077257..29078903-chr18:29144506..29147477,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000046604	Chromatin interaction

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

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

rs_ID	r²[population]
rs10468828	0.80[EUR][1000 genomes]
rs1551001	0.80[EUR][1000 genomes]
rs1551002	0.95[EUR][1000 genomes]
rs1551003	0.82[EUR][1000 genomes]
rs1551004	0.83[EUR][1000 genomes]
rs1667225	0.92[EUR][1000 genomes]
rs1667229	0.96[EUR][1000 genomes]
rs1667230	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1667234	1.00[EUR][1000 genomes]
rs1667235	1.00[EUR][1000 genomes]
rs1791208	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1791209	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1791212	0.96[EUR][1000 genomes]
rs1791215	0.80[EUR][1000 genomes]
rs1791218	1.00[EUR][1000 genomes]
rs1941931	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4315413	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs875425	0.96[EUR][1000 genomes]
rs875426	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs877597	0.80[EUR][1000 genomes]
rs9304102	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9951041	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9963742	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9963820	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv576635	chr18:29129931-29148814	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv576636	chr18:29146822-29190174	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv21155	chr18:29146941-29148053	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29144200-29147600	Enhancers	Fetal Intestine Large	intestine
2	chr18:29145400-29147600	Enhancers	Fetal Intestine Small	intestine
3	chr18:29146000-29147200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr18:29146200-29147000	Enhancers	Duodenum Mucosa	Duodenum
5	chr18:29146200-29147000	Flanking Active TSS	HepG2	liver
6	chr18:29146600-29147000	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr18:29146600-29147400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr18:29146600-29156600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr18:29146800-29147000	Enhancers	Colonic Mucosa	Colon
10	chr18:29146800-29147000	Bivalent Enhancer	Stomach Mucosa	stomach
11	chr18:29146800-29147200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr18:29146800-29147800	Enhancers	Liver	Liver

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