Variant report

Variant	rs9807444
Chromosome Location	chr18:12300936-12300937
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	chr18:12300402..12301963-chr18:12307170..12309315,2	MCF-7	breast:
2	chr18:12300205..12301767-chr18:12360649..12362884,2	K562	blood:

Variant related genes	Relation type
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10853224	1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11080567	1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11267036	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11548177	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11659246	0.93[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[EUR][1000 genomes]
rs11660106	0.83[EUR][1000 genomes]
rs11660222	1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11661431	0.80[ASN][1000 genomes]
rs11663340	0.93[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[EUR][1000 genomes]
rs11664255	0.83[EUR][1000 genomes]
rs11664282	0.83[EUR][1000 genomes]
rs12455756	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12455885	0.81[ASN][1000 genomes]
rs12607250	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12607321	1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12607378	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12954560	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12959674	0.80[ASN][1000 genomes]
rs12960267	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12960302	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs12963761	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12965912	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12970667	0.93[CHB][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs28625182	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34685983	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35242253	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35959277	0.84[ASN][1000 genomes]
rs4796958	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4796959	0.82[ASN][1000 genomes]
rs4796960	1.00[CEU][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4796962	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4796963	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4797673	1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4797674	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4797675	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58136410	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61604633	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62097556	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505749	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505751	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7231304	0.93[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.83[EUR][1000 genomes]
rs7233290	0.83[EUR][1000 genomes]
rs7244254	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7244709	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7504558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7504575	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7504616	0.83[EUR][1000 genomes]
rs7505208	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7505255	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7505626	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8083882	1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8087843	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8098040	0.87[CHD][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8099636	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9303766	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9303767	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9303768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9652931	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9945901	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9946172	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9946217	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9946347	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9949054	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9954945	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9958069	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9958525	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9964163	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9966470	0.93[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9807444	MGC4083	cis	multi-tissue	Pritchard
rs9807444	TUBB6	cis	multi-tissue	Pritchard
rs9807444	TUBB6	cis	lymphoblastoid	GTEx
rs9807444	TUBB6	cis	lymphoblastoid	seeQTL
rs9807444	TUBB6	cis	Lymphoblastoid	GTEx
rs9807444	TUBB6	cis	Whole Blood	GTEx

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	chr18:12298400-12301000	Weak transcription	Fetal Heart	heart
9	chr18:12300600-12302200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr18:12300600-12302400	Enhancers	K562	blood

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