Variant report

Variant	rs12456857
Chromosome Location	chr18:12301395-12301396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12287873..12290167-chr18:12301224..12302973,2	MCF-7	breast:
2	chr18:12300402..12301963-chr18:12307170..12309315,2	MCF-7	breast:
3	chr18:12300205..12301767-chr18:12360649..12362884,2	K562	blood:
4	chr18:12300999..12303281-chr18:12308137..12310057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267069	Chromatin interaction
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10459999	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10460000	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10460001	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11080564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11080565	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11080569	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11080571	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11080572	0.95[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1129115	0.95[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11662523	0.95[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs11664216	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11665134	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11875938	0.83[EUR][1000 genomes]
rs12455273	0.83[EUR][1000 genomes]
rs12455770	0.88[EUR][1000 genomes]
rs12604732	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12954686	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12968566	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1941222	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs2298542	0.80[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs2298543	0.80[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs28372882	0.83[EUR][1000 genomes]
rs34314823	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34829762	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35338639	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3786260	0.83[ASW][hapmap];0.80[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs478088	0.80[CEU][hapmap]
rs4796961	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4796964	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4797672	0.84[AFR][1000 genomes]
rs4797677	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs4797680	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs62098961	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7231182	0.95[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs7231409	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7235237	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7235296	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7407640	0.95[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs7504908	0.95[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7504974	0.95[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7505834	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8086821	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8086993	1.00[ASW][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8087840	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8092506	1.00[CEU][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8097342	0.84[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs9303769	0.95[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs9303770	0.83[ASW][hapmap];0.80[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs9946698	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9951945	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9956171	0.80[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
rs12456857	TUBB6	cis	lymphoblastoid	seeQTL
rs12456857	TUBB6	cis	Whole Blood	GTEx
rs12456857	MEST	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12289000-12304800	Weak transcription	Pancreas	Pancrea
2	chr18:12289200-12306400	Weak transcription	Right Atrium	heart
3	chr18:12289400-12306400	Weak transcription	NHLF	lung
4	chr18:12291600-12301600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr18:12294400-12306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:12296800-12302000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr18:12297200-12302000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr18:12300600-12302200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr18:12300600-12302400	Enhancers	K562	blood
10	chr18:12301000-12303000	Enhancers	Fetal Heart	heart

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