Variant report

Variant	rs12954560
Chromosome Location	chr18:12292543-12292544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12291981..12293994-chr18:12306663..12308783,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11267036	0.84[EUR][1000 genomes]
rs11548177	0.86[EUR][1000 genomes]
rs11661431	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12455756	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12455885	0.83[ASN][1000 genomes]
rs12607250	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12960267	0.84[EUR][1000 genomes]
rs12960302	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12963761	0.86[EUR][1000 genomes]
rs12965912	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28625182	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34685983	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35959277	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4796963	0.84[EUR][1000 genomes]
rs58136410	0.84[EUR][1000 genomes]
rs61604633	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62097556	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6505746	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6505749	0.84[EUR][1000 genomes]
rs7244709	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7504558	0.86[EUR][1000 genomes]
rs7504575	0.86[EUR][1000 genomes]
rs7505255	0.84[EUR][1000 genomes]
rs7505626	0.84[EUR][1000 genomes]
rs8087843	0.84[EUR][1000 genomes]
rs9303766	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9303767	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9303768	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9652931	0.84[EUR][1000 genomes]
rs9807444	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9945901	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9946172	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9946217	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9946347	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9949054	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9954945	0.86[ASN][1000 genomes]
rs9958069	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9958525	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9964163	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv870342	chr18:12270808-12295798	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12954560	TUBB6	cis	Whole Blood	GTEx
rs12954560	MC1R///TUBB3	trans	lymphoblastoid	RTeQTL
rs12954560	TUBB6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12288400-12296200	Weak transcription	Spleen	Spleen
2	chr18:12289000-12292600	Weak transcription	Aorta	Aorta
3	chr18:12289000-12304800	Weak transcription	Pancreas	Pancrea
4	chr18:12289200-12294000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:12289200-12306400	Weak transcription	Right Atrium	heart
6	chr18:12289400-12295600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr18:12289400-12298200	Weak transcription	Fetal Heart	heart
8	chr18:12289400-12306400	Weak transcription	NHLF	lung
9	chr18:12290200-12295400	Weak transcription	NHDF-Ad	bronchial
10	chr18:12290400-12293800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr18:12290400-12294600	Weak transcription	HMEC	breast
12	chr18:12290400-12295800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr18:12290400-12296000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr18:12290400-12296000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr18:12291600-12301600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr18:12292000-12294000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr18:12292000-12294000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr18:12292000-12295800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:12292200-12294200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr18:12292200-12295600	Weak transcription	K562	blood

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