Variant report

Variant	rs17269643
Chromosome Location	chr15:59850228-59850229
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59848605..59850889-chr15:59851125..59852775,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12591916	0.81[CEU][hapmap];0.90[GIH][hapmap]
rs17269649	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450345	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28465501	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28642985	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4334235	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55646727	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55650268	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55677374	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55724601	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55895417	0.84[EUR][1000 genomes]
rs56252156	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56305024	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59344823	0.83[EUR][1000 genomes]
rs67098767	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176379	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181219	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181242	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72749183	0.83[ASN][1000 genomes]
rs72749188	0.83[ASN][1000 genomes]
rs72749190	0.83[ASN][1000 genomes]
rs72751123	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv527754	chr15:59848471-59855226	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17269643	TCF12	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59841600-59861600	Weak transcription	Gastric	stomach
2	chr15:59843600-59851200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:59848400-59851000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:59848400-59851000	Weak transcription	Osteobl	bone
5	chr15:59848800-59850600	Weak transcription	Fetal Intestine Small	intestine
6	chr15:59848800-59850600	Weak transcription	A549	lung
7	chr15:59848800-59851200	Enhancers	Hela-S3	cervix
8	chr15:59848800-59851400	Weak transcription	Stomach Mucosa	stomach
9	chr15:59848800-59857600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:59849000-59850800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:59849000-59853600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:59849200-59850600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:59849400-59851200	Weak transcription	Small Intestine	intestine
14	chr15:59850000-59850800	Enhancers	GM12878-XiMat	blood
15	chr15:59850000-59851200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr15:59850200-59853200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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