Variant report

Variant	rs7178452
Chromosome Location	chr15:44242039-44242040
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:44237370..44240153-chr15:44241264..44242889,2	K562	blood:
2	chr15:44240850..44243740-chr15:44243781..44246529,3	K562	blood:
3	chr15:44240850..44243740-chr15:44243781..44246073,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1008183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152658	0.82[EUR][1000 genomes]
rs1077421	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11070413	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070416	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11630936	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11635039	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11637468	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12439442	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12440402	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12442168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16944774	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs16945686	1.00[CEU][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16950215	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2306674	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28377221	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28438984	0.97[EUR][1000 genomes]
rs28525216	1.00[TSI][hapmap]
rs28542819	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28599486	0.97[EUR][1000 genomes]
rs28670868	0.83[EUR][1000 genomes]
rs28685813	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28697876	0.81[MEX][hapmap]
rs28706414	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3742981	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3850777	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55927923	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60484809	0.91[EUR][1000 genomes]
rs8031749	0.83[EUR][1000 genomes]
rs9806129	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9920164	1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][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	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7178452	LOC440278	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44225400-44246200	Weak transcription	Right Atrium	heart
2	chr15:44225600-44246200	Weak transcription	NH-A	brain
3	chr15:44227200-44251000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:44227400-44244200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:44229000-44245000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:44235000-44242400	Weak transcription	Brain Substantia Nigra	brain
7	chr15:44236400-44246200	Weak transcription	NHLF	lung
8	chr15:44238200-44245800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:44239200-44242200	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:44239200-44242800	Weak transcription	Fetal Heart	heart
11	chr15:44240400-44242200	Weak transcription	Brain Anterior Caudate	brain
12	chr15:44240400-44243800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:44241200-44243000	Enhancers	Brain Cingulate Gyrus	brain
14	chr15:44241400-44243000	Enhancers	Brain Angular Gyrus	brain
15	chr15:44241600-44246000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:44241800-44242800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:44241800-44243000	Enhancers	GM12878-XiMat	blood
18	chr15:44242000-44243000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:44242000-44250400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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