Variant report

Variant	rs11740589
Chromosome Location	chr5:154212485-154212486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr5:154212410-154212773	K562	blood:	n/a	n/a
2	JUND	chr5:154212435-154212722	K562	blood:	n/a	chr5:154212553-154212562
3	JUND	chr5:154212392-154212713	HepG2	liver:	n/a	chr5:154212553-154212562
4	JUN	chr5:154212482-154212682	HepG2	liver:	n/a	chr5:154212552-154212565 chr5:154212553-154212562

No.	Distal block	Cell Line	Cell type
1	chr5:154207634..154212086-chr5:154212438..154216728,14	MCF-7	breast:
2	chr5:154205913..154219158-chr5:154234172..154242635,38	MCF-7	breast:
3	chr5:154121511..154123647-chr5:154211048..154213983,2	K562	blood:
4	chr5:154211040..154212734-chr5:154289687..154291333,2	K562	blood:

Variant related genes	Relation type
FAXDC2	TF binding region
ENSG00000155508	Chromatin interaction
ENSG00000263361	Chromatin interaction
ENSG00000170271	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10515726	0.86[YRI][hapmap]
rs11740031	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11743080	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs286595	0.93[ASW][hapmap];0.85[CEU][hapmap];0.89[GIH][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs286596	0.84[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs348735	0.83[GIH][hapmap];0.82[YRI][hapmap]
rs3853757	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3867429	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs3867430	0.86[YRI][hapmap]
rs55849543	1.00[ASN][1000 genomes]
rs6863954	1.00[ASN][1000 genomes]
rs72797583	1.00[ASN][1000 genomes]
rs7328	0.88[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes]
rs7710726	1.00[ASN][1000 genomes]
rs7734591	1.00[ASN][1000 genomes]
rs903837	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11740589	LARP1	cis	multi-tissue	Pritchard
rs11740589	LARP1	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154195600-154214400	Weak transcription	Small Intestine	intestine
2	chr5:154196000-154229200	Weak transcription	Psoas Muscle	Psoas
3	chr5:154196400-154214000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:154197600-154214400	Weak transcription	HUVEC	blood vessel
5	chr5:154197800-154214400	Weak transcription	Hela-S3	cervix
6	chr5:154199400-154214400	Weak transcription	Right Atrium	heart
7	chr5:154200200-154214400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:154200800-154214000	Weak transcription	Fetal Heart	heart
9	chr5:154201000-154228000	Weak transcription	Fetal Brain Male	brain
10	chr5:154203400-154229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:154203600-154214400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:154204200-154214400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:154204400-154213800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr5:154204400-154213800	Weak transcription	NHDF-Ad	bronchial
15	chr5:154204400-154214400	Weak transcription	Brain Germinal Matrix	brain
16	chr5:154206400-154212800	Strong transcription	Brain Anterior Caudate	brain
17	chr5:154208600-154212600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:154208800-154212600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:154209400-154214000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:154209400-154214400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:154209800-154214000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:154210000-154213800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr5:154210000-154214200	Weak transcription	Placenta	Placenta
24	chr5:154210000-154214200	Weak transcription	Stomach Mucosa	stomach
25	chr5:154210000-154214200	Weak transcription	NH-A	brain
26	chr5:154210000-154214400	Weak transcription	Colonic Mucosa	Colon
27	chr5:154210200-154213200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:154210200-154214600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:154210200-154229000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:154210400-154213800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:154210400-154214000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:154210400-154214400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:154210600-154213600	Weak transcription	Primary T cells from cord blood	blood
34	chr5:154210600-154213800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr5:154210600-154213800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:154210600-154213800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr5:154210600-154214000	Weak transcription	GM12878-XiMat	blood
38	chr5:154210600-154214200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr5:154210600-154214200	Weak transcription	Lung	lung
40	chr5:154210600-154214200	Weak transcription	Ovary	ovary
41	chr5:154210600-154214200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr5:154210600-154214200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr5:154210600-154214400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:154210600-154215000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr5:154210800-154213600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr5:154210800-154214200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:154210800-154214200	Weak transcription	HSMMtube	muscle
48	chr5:154210800-154214400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:154210800-154214400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr5:154210800-154229000	Weak transcription	Fetal Kidney	kidney

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