Variant report

Variant	rs6886571
Chromosome Location	chr5:154150451-154150452
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154135565..154137927-chr5:154149655..154152565,3	MCF-7	breast:
2	chr5:154141399..154144040-chr5:154148555..154150698,2	MCF-7	breast:
3	chr5:154132476..154143251-chr5:154145354..154162500,38	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10515726	0.82[AMR][1000 genomes]
rs11167702	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948782	0.87[ASN][1000 genomes]
rs17641488	0.87[ASN][1000 genomes]
rs34951340	0.87[ASN][1000 genomes]
rs3867430	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55734017	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56226335	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6886571	LARP1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154138200-154151400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr5:154138200-154156000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr5:154141200-154150600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:154141200-154151000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:154141400-154152200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:154143200-154150600	Enhancers	Primary B cells from peripheral blood	blood
7	chr5:154144400-154151800	Genic enhancers	K562	blood
8	chr5:154144600-154150800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:154144600-154151600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr5:154144600-154151600	Enhancers	Brain Anterior Caudate	brain
11	chr5:154144600-154151600	Enhancers	Left Ventricle	heart
12	chr5:154144600-154157200	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr5:154144800-154150800	Enhancers	Primary B cells from cord blood	blood
14	chr5:154145000-154150600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:154145400-154151600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:154145800-154150800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:154146600-154153800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:154147400-154161800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr5:154147600-154150600	Weak transcription	NH-A	brain
20	chr5:154147600-154150800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr5:154147600-154150800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:154147600-154151600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr5:154147800-154150600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:154148200-154150600	Enhancers	Lung	lung
25	chr5:154148200-154151400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:154148200-154151400	Enhancers	Esophagus	oesophagus
27	chr5:154148200-154151600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:154148200-154151600	Enhancers	Psoas Muscle	Psoas
29	chr5:154148200-154155800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:154148400-154150800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:154148400-154150800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr5:154148400-154151400	Enhancers	Liver	Liver
33	chr5:154148400-154151400	Enhancers	Fetal Heart	heart
34	chr5:154148400-154151400	Enhancers	Spleen	Spleen
35	chr5:154148400-154151600	Enhancers	Brain Hippocampus Middle	brain
36	chr5:154148400-154151600	Enhancers	Brain Substantia Nigra	brain
37	chr5:154148400-154152000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr5:154148400-154153000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr5:154148400-154154200	Enhancers	Adipose Nuclei	Adipose
40	chr5:154148400-154155400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr5:154148400-154156000	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr5:154148600-154150600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:154148600-154150600	Enhancers	Pancreas	Pancrea
44	chr5:154148600-154150800	Enhancers	Primary hematopoietic stem cells	blood
45	chr5:154148600-154150800	Enhancers	Brain Cingulate Gyrus	brain
46	chr5:154148600-154150800	Enhancers	Colon Smooth Muscle	Colon
47	chr5:154148600-154150800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr5:154148600-154150800	Enhancers	Stomach Smooth Muscle	stomach
49	chr5:154148600-154151000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:154148600-154151000	Enhancers	Fetal Brain Female	brain

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