Variant report

Variant	rs4534617
Chromosome Location	chr12:60334109-60334110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10160895	0.90[EUR][1000 genomes]
rs10160973	0.83[EUR][1000 genomes]
rs10161437	0.83[EUR][1000 genomes]
rs10735882	0.89[EUR][1000 genomes]
rs10747861	0.90[EUR][1000 genomes]
rs10784010	0.83[EUR][1000 genomes]
rs10784014	0.90[EUR][1000 genomes]
rs10784015	0.90[EUR][1000 genomes]
rs10784022	0.80[EUR][1000 genomes]
rs10877360	0.83[EUR][1000 genomes]
rs10877361	0.83[EUR][1000 genomes]
rs10877362	0.83[EUR][1000 genomes]
rs10877363	0.83[EUR][1000 genomes]
rs10877364	0.82[EUR][1000 genomes]
rs10877365	0.90[EUR][1000 genomes]
rs11173205	0.83[EUR][1000 genomes]
rs11173206	0.82[EUR][1000 genomes]
rs11173207	0.83[EUR][1000 genomes]
rs11173208	0.83[EUR][1000 genomes]
rs11173212	0.83[EUR][1000 genomes]
rs11173217	0.83[EUR][1000 genomes]
rs11173225	0.90[EUR][1000 genomes]
rs11173226	0.90[EUR][1000 genomes]
rs11173227	0.90[EUR][1000 genomes]
rs11173228	0.90[EUR][1000 genomes]
rs11173229	0.90[EUR][1000 genomes]
rs11173231	0.89[EUR][1000 genomes]
rs11173233	0.90[EUR][1000 genomes]
rs11173268	0.82[EUR][1000 genomes]
rs11173276	0.80[EUR][1000 genomes]
rs11173302	0.80[EUR][1000 genomes]
rs11609497	0.90[EUR][1000 genomes]
rs11609524	0.90[EUR][1000 genomes]
rs12303323	0.83[EUR][1000 genomes]
rs12304178	0.83[EUR][1000 genomes]
rs12309079	0.83[EUR][1000 genomes]
rs12309131	0.83[EUR][1000 genomes]
rs12320040	0.83[EUR][1000 genomes]
rs12322528	0.83[EUR][1000 genomes]
rs12322648	0.83[EUR][1000 genomes]
rs12370452	0.90[EUR][1000 genomes]
rs12372035	0.90[EUR][1000 genomes]
rs12423658	0.89[EUR][1000 genomes]
rs12820688	0.89[EUR][1000 genomes]
rs1602835	0.80[EUR][1000 genomes]
rs34089860	0.82[EUR][1000 genomes]
rs34528640	0.82[EUR][1000 genomes]
rs34615410	0.83[EUR][1000 genomes]
rs35425604	0.82[EUR][1000 genomes]
rs4288788	0.90[EUR][1000 genomes]
rs4291710	0.90[EUR][1000 genomes]
rs4363643	0.82[EUR][1000 genomes]
rs4492855	0.90[EUR][1000 genomes]
rs4614493	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4623940	0.83[EUR][1000 genomes]
rs4758736	0.82[EUR][1000 genomes]
rs4758874	0.90[EUR][1000 genomes]
rs4758878	0.90[EUR][1000 genomes]
rs4758879	0.90[EUR][1000 genomes]
rs5026694	0.83[EUR][1000 genomes]
rs61935612	0.83[EUR][1000 genomes]
rs6581285	0.90[EUR][1000 genomes]
rs7303843	0.82[EUR][1000 genomes]
rs7954965	0.82[EUR][1000 genomes]
rs9943708	0.86[EUR][1000 genomes]
rs9943716	0.87[EUR][1000 genomes]
rs9943772	0.83[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	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2751107	chr12:60252000-60353533	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv826393	chr12:60293625-60359283	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4534617	GTSF1	cis	parietal	SCAN
rs4534617	TAC3	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60331400-60334400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:60332600-60334400	Enhancers	A549	lung
3	chr12:60333000-60334600	Enhancers	Fetal Lung	lung
4	chr12:60333200-60334800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:60333400-60334600	Weak transcription	Fetal Heart	heart
6	chr12:60333600-60335000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:60333600-60336200	Enhancers	Fetal Intestine Small	intestine
8	chr12:60333800-60334200	Enhancers	Fetal Intestine Large	intestine
9	chr12:60334000-60334200	Enhancers	HUES64 Cell Line	embryonic stem cell

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