Variant report

Variant	rs6440136
Chromosome Location	chr3:142852015-142852016
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	chr3:142851820..142854133-chr3:142856452..142858967,2	MCF-7	breast:
2	chr3:142850270..142855258-chr3:142857254..142859835,5	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10084718	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1056360	0.97[EUR][1000 genomes]
rs1134685	0.97[EUR][1000 genomes]
rs11710763	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11711866	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11718140	0.96[CEU][hapmap]
rs11719768	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1597389	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16853045	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1900994	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1900995	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4683448	0.96[CEU][hapmap]
rs4683449	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4683450	0.84[ASN][1000 genomes]
rs4683451	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683452	0.88[ASN][1000 genomes]
rs4683454	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4683455	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4683741	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683743	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4683744	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4683745	0.93[EUR][1000 genomes]
rs4683746	0.93[EUR][1000 genomes]
rs4683747	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4683748	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440137	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440141	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440142	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66726727	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67496487	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67627912	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6770489	0.96[CEU][hapmap]
rs6789472	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6794836	0.96[CEU][hapmap]
rs6801537	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6801610	0.81[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6805732	0.81[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs68171708	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs726737	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73159623	0.95[EUR][1000 genomes]
rs735564	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9829651	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1007164	chr3:142837004-142891719	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv508250	chr3:142842454-142943722	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6440136	MESP1	cis	Frontal Cortex	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142840600-142854600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:142841200-142852800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:142841200-142853200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:142841200-142858000	Weak transcription	Spleen	Spleen
5	chr3:142844000-142853200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:142844200-142853400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:142844600-142853000	Weak transcription	Primary B cells from cord blood	blood
8	chr3:142844600-142853200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:142844800-142852600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr3:142844800-142858200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:142845800-142858200	Weak transcription	Fetal Brain Male	brain
12	chr3:142846800-142852400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:142847200-142852600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:142847200-142853400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:142847400-142853400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:142848200-142853200	Weak transcription	NHLF	lung
17	chr3:142849200-142854200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:142850200-142853200	Weak transcription	Fetal Lung	lung
19	chr3:142850400-142853400	Weak transcription	Fetal Brain Female	brain
20	chr3:142851200-142853400	Weak transcription	HSMMtube	muscle
21	chr3:142851600-142852800	Genic enhancers	Primary T cells from cord blood	blood
22	chr3:142851800-142853800	Enhancers	K562	blood
23	chr3:142852000-142852400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:142852000-142852400	Enhancers	Fetal Thymus	thymus
25	chr3:142852000-142853400	Weak transcription	GM12878-XiMat	blood
26	chr3:142852000-142856600	Weak transcription	Dnd41	blood

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