Variant report

Variant	rs55696942
Chromosome Location	chr5:42570941-42570942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42557269..42559251-chr5:42568041..42570943,2	MCF-7	breast:
2	chr5:42565617..42568095-chr5:42569721..42572665,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112964	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10941578	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10941579	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739444	0.86[EUR][1000 genomes]
rs11740415	0.86[EUR][1000 genomes]
rs11949751	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955075	0.86[EUR][1000 genomes]
rs12516901	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12520276	0.95[ASN][1000 genomes]
rs12521020	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13176410	0.91[EUR][1000 genomes]
rs28943881	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34374598	0.90[EUR][1000 genomes]
rs34466913	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34535288	0.93[EUR][1000 genomes]
rs34895721	0.86[EUR][1000 genomes]
rs35090794	0.90[EUR][1000 genomes]
rs4075783	0.91[ASN][1000 genomes]
rs4365846	0.92[EUR][1000 genomes]
rs4368736	0.92[EUR][1000 genomes]
rs4395642	0.92[EUR][1000 genomes]
rs4489074	0.92[ASN][1000 genomes]
rs4496716	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4504390	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4533898	0.92[ASN][1000 genomes]
rs61197005	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6865492	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896667	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7707913	0.86[EUR][1000 genomes]
rs7712701	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7714392	0.95[EUR][1000 genomes]
rs7735889	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736209	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42565800-42571000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:42566000-42571000	Weak transcription	HMEC	breast
3	chr5:42566000-42571200	Weak transcription	Psoas Muscle	Psoas
4	chr5:42566000-42576200	Weak transcription	Spleen	Spleen
5	chr5:42566200-42571000	Weak transcription	NHEK	skin
6	chr5:42566200-42571200	Weak transcription	Left Ventricle	heart
7	chr5:42566800-42571000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:42567400-42571200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:42567600-42571200	Weak transcription	Aorta	Aorta
10	chr5:42567800-42571000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:42568000-42571200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:42568000-42571400	Weak transcription	Adipose Nuclei	Adipose
13	chr5:42568000-42571400	Weak transcription	HSMMtube	muscle
14	chr5:42568000-42579400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:42568000-42581400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:42568000-42582200	Weak transcription	Fetal Intestine Small	intestine
17	chr5:42568400-42571200	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:42568400-42571200	Weak transcription	Right Atrium	heart
19	chr5:42568400-42571200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:42568400-42571200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:42568400-42581800	Weak transcription	Fetal Stomach	stomach
22	chr5:42568400-42582800	Weak transcription	Ovary	ovary
23	chr5:42568800-42571200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:42568800-42571200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:42569400-42571000	Weak transcription	Fetal Lung	lung
26	chr5:42569400-42572200	Enhancers	Liver	Liver
27	chr5:42570000-42571400	Enhancers	Fetal Heart	heart
28	chr5:42570200-42571800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:42570200-42572800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:42570600-42571000	Weak transcription	Right Ventricle	heart
31	chr5:42570800-42572000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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