Variant report

Variant	rs12654102
Chromosome Location	chr5:1962436-1962437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:1955843..1957628-chr5:1960961..1962792,2	K562	blood:
2	chr5:1961890..1964655-chr5:1980706..1982291,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10035144	0.83[ASN][1000 genomes]
rs10045683	0.82[ASN][1000 genomes]
rs10053882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10066840	0.85[AFR][1000 genomes]
rs1017924	0.83[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs11133918	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs1123381	0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs1123390	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs1123391	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs11952205	0.81[ASN][1000 genomes]
rs12188545	0.81[ASN][1000 genomes]
rs12716127	0.83[ASN][1000 genomes]
rs13166888	0.82[ASN][1000 genomes]
rs13170991	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1906179	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4246751	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4246752	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs4371796	0.82[ASN][1000 genomes]
rs4382203	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4407661	0.83[ASN][1000 genomes]
rs4975777	0.83[ASN][1000 genomes]
rs55860207	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57434783	0.83[ASN][1000 genomes]
rs62337105	0.94[AFR][1000 genomes]
rs67659713	0.82[ASN][1000 genomes]
rs7445193	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs872807	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs901504	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][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	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv508344	chr5:1905222-1976860	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv881562	chr5:1907974-1976187	Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	esv3417599	chr5:1959252-1962550	ZNF genes & repeats Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3382780	chr5:1959452-1962650	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12654102	TRIP13	cis	parietal	SCAN
rs12654102	TPPP	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1939000-1965600	Weak transcription	Brain Angular Gyrus	brain
2	chr5:1950600-1963800	Weak transcription	Right Ventricle	heart
3	chr5:1954000-1962600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:1955000-1965800	Weak transcription	Adipose Nuclei	Adipose
5	chr5:1958200-1966800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:1961200-1967800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:1961400-1963200	Weak transcription	Pancreas	Pancrea
8	chr5:1961400-1963600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:1961400-1964600	Enhancers	HMEC	breast
10	chr5:1961600-1965800	Weak transcription	Dnd41	blood
11	chr5:1961800-1964400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:1962000-1963400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:1962000-1963800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:1962000-1964000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:1962200-1963800	Enhancers	NHEK	skin
16	chr5:1962400-1962600	Enhancers	Esophagus	oesophagus
17	chr5:1962400-1964400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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