Variant report

Variant	rs10455076
Chromosome Location	chr5:178213713-178213714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178211735..178215494-chr5:178218190..178221753,4	MCF-7	breast:
2	chr5:177630127..177632197-chr5:178212770..178214294,2	MCF-7	breast:
3	chr5:177659037..177660828-chr5:178212887..178215227,2	MCF-7	breast:
4	chr5:178155431..178159106-chr5:178210602..178214832,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169131	Chromatin interaction
ENSG00000175309	Chromatin interaction
ENSG00000197451	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10038743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10039698	0.84[AFR][1000 genomes]
rs10041558	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10041561	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10044101	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10070226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10077060	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs10455073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10455074	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10455075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10455077	0.87[EUR][1000 genomes]
rs12518917	0.85[EUR][1000 genomes]
rs56394232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57871332	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59612625	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60286346	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62393895	0.87[EUR][1000 genomes]
rs62393896	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62393901	0.85[EUR][1000 genomes]
rs72812691	0.81[EUR][1000 genomes]
rs7444300	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs9329054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9329055	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[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	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031206	chr5:178149292-178283614	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537973	chr5:178149292-178283614	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv462573	chr5:178180299-178241495	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv600452	chr5:178180299-178241495	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10455076	MXD3	cis	parietal	SCAN
rs10455076	GNB2L1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178166600-178224000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:178206400-178217600	Weak transcription	Gastric	stomach
3	chr5:178210600-178214000	Weak transcription	Fetal Kidney	kidney
4	chr5:178210600-178217400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:178212200-178214000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:178212800-178214600	Enhancers	Osteobl	bone
7	chr5:178213000-178215200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:178213200-178213800	Enhancers	Esophagus	oesophagus
9	chr5:178213200-178214200	Flanking Active TSS	A549	lung
10	chr5:178213200-178215000	Enhancers	K562	blood
11	chr5:178213200-178215800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr5:178213200-178215800	Enhancers	Stomach Mucosa	stomach
13	chr5:178213400-178215200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:178213400-178215200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:178213600-178214000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:178213600-178214000	Bivalent Enhancer	HepG2	liver
17	chr5:178213600-178214200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:178213600-178214200	Enhancers	HMEC	breast
19	chr5:178213600-178214200	Enhancers	NHEK	skin
20	chr5:178213600-178214600	Enhancers	Fetal Intestine Small	intestine

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