Variant report

Variant	rs17625129
Chromosome Location	chr13:30281760-30281761
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:30081966..30082930-chr13:30281642..30282704,6	MCF-7	breast:
2	chr13:30081784..30083540-chr13:30281671..30282678,17	MCF-7	breast:
3	chr13:30046058..30047280-chr13:30281639..30283052,17	MCF-7	breast:
4	chr13:30163838..30166172-chr13:30279497..30282436,2	K562	blood:
5	chr13:30167909..30169969-chr13:30279599..30282032,2	MCF-7	breast:
6	chr13:30277466..30279182-chr13:30280230..30281959,2	MCF-7	breast:
7	chr13:30022231..30024197-chr13:30280852..30283786,2	K562	blood:
8	chr13:30046073..30047178-chr13:30281732..30282586,7	MCF-7	breast:
9	chr13:30276744..30278789-chr13:30280944..30283697,2	K562	blood:
10	chr13:30082009..30082874-chr13:30281689..30282679,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139514	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1010154	0.84[ASN][1000 genomes]
rs12854213	0.84[ASN][1000 genomes]
rs12870250	0.85[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs12870927	0.85[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1467601	0.95[ASN][1000 genomes]
rs1590696	0.87[ASN][1000 genomes]
rs1752040	0.87[ASN][1000 genomes]
rs2078408	0.85[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2388241	0.81[ASN][1000 genomes]
rs34053860	0.92[ASN][1000 genomes]
rs3858738	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4769767	0.87[ASN][1000 genomes]
rs4769768	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4769769	0.84[ASN][1000 genomes]
rs6490421	0.81[ASN][1000 genomes]
rs6490422	0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs6490423	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6490424	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7317991	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7318002	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7323986	0.93[ASN][1000 genomes]
rs7324910	0.93[ASN][1000 genomes]
rs7328052	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7333892	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7337296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7991022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9506220	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9508530	0.81[ASN][1000 genomes]
rs9508532	0.83[ASN][1000 genomes]
rs9508533	0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs9508534	0.85[ASN][1000 genomes]
rs9508535	0.85[ASN][1000 genomes]
rs9508536	0.87[ASN][1000 genomes]
rs9508537	0.87[ASN][1000 genomes]
rs9508538	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs9508539	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9508540	0.98[ASN][1000 genomes]
rs9508541	0.87[ASN][1000 genomes]
rs9550489	0.87[ASN][1000 genomes]
rs9551721	0.97[ASN][1000 genomes]
rs9551722	0.84[ASN][1000 genomes]
rs9579471	0.84[ASN][1000 genomes]
rs9634355	0.87[ASN][1000 genomes]
rs997896	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30278800-30283400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr13:30279000-30281800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr13:30279600-30281800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:30280200-30282800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:30280400-30284600	Weak transcription	Esophagus	oesophagus
6	chr13:30280600-30282600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:30281200-30282000	Enhancers	Stomach Smooth Muscle	stomach
8	chr13:30281600-30282000	Enhancers	Spleen	Spleen
9	chr13:30281600-30282400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr13:30281600-30282600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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