Variant report

Variant	rs3781909
Chromosome Location	chr11:73356872-73356873
allele	C/T
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	CTBP2	chr11:73356696-73357773	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:73356593-73357696	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr11:73356845-73357572	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr11:73356737-73357643	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3A	chr11:73356588-73357771	H1-hESC	embryonic stem cell:	n/a	chr11:73356842-73356855 chr11:73357274-73357287
6	YY1	chr11:73356810-73357463	H1-hESC	embryonic stem cell:	n/a	chr11:73357310-73357319 chr11:73357244-73357258
7	POLR2A	chr11:73356852-73357554	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73307696..73311155-chr11:73356118..73358808,4	MCF-7	breast:

Variant related genes	Relation type
PLEKHB1	TF binding region
ENSG00000054965	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10128692	0.82[AMR][1000 genomes]
rs10793063	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10793064	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10793065	0.83[CHB][hapmap];0.84[YRI][hapmap]
rs11235828	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235830	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525749	0.92[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1976911	0.86[AMR][1000 genomes]
rs2008734	0.92[ASW][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3817514	0.95[CHB][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3862797	0.91[CHB][hapmap];0.86[AMR][1000 genomes]
rs680901	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7103745	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1045149	chr11:73314565-73581908	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv525173	chr11:73356872-73364673	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3781909	MRPL48	cis	multi-tissue	Pritchard
rs3781909	WDR71	cis	multi-tissue	Pritchard
rs3781909	MOGAT2	cis	cerebellum	SCAN
rs3781909	PLEKHB1	cis	parietal	SCAN
rs3781909	MRPL48	cis	cerebellum	SCAN
rs3781909	MRPL48	Cis_1M	lymphoblastoid	RTeQTL
rs3781909	MRPL48	cis	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73350000-73358600	Weak transcription	Right Atrium	heart
2	chr11:73352000-73357400	Weak transcription	Primary T cells from cord blood	blood
3	chr11:73352000-73358000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr11:73352800-73357600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr11:73353000-73357800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr11:73353000-73358200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr11:73356000-73357400	Bivalent Enhancer	Fetal Intestine Small	intestine
8	chr11:73356200-73357000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:73356200-73357000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr11:73356200-73357200	Bivalent Enhancer	Fetal Stomach	stomach
11	chr11:73356200-73357400	Enhancers	HepG2	liver
12	chr11:73356200-73357600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr11:73356200-73358000	Bivalent Enhancer	Fetal Thymus	thymus
14	chr11:73356200-73358600	Enhancers	Placenta	Placenta
15	chr11:73356200-73358800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:73356200-73360800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:73356400-73357000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
18	chr11:73356400-73357000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
19	chr11:73356400-73357000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr11:73356400-73357000	Bivalent/Poised TSS	NHEK	skin
21	chr11:73356400-73357200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:73356400-73357200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
23	chr11:73356400-73357200	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr11:73356400-73357400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr11:73356400-73357800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr11:73356400-73357800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:73356400-73357800	Bivalent Enhancer	Fetal Intestine Large	intestine
28	chr11:73356600-73357000	Enhancers	Fetal Kidney	kidney
29	chr11:73356600-73357200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr11:73356600-73357200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:73356600-73357200	Bivalent Enhancer	Adipose Nuclei	Adipose
32	chr11:73356600-73357200	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr11:73356600-73357200	Enhancers	Fetal Heart	heart
34	chr11:73356600-73357200	Bivalent Enhancer	Fetal Lung	lung
35	chr11:73356600-73357200	Bivalent Enhancer	HUVEC	blood vessel
36	chr11:73356600-73357400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:73356600-73357400	Bivalent Enhancer	NHDF-Ad	bronchial
38	chr11:73356600-73357600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr11:73356600-73357800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr11:73356600-73358400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr11:73356600-73358600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr11:73356600-73358600	Enhancers	Right Ventricle	heart
43	chr11:73356600-73359000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr11:73356600-73359000	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr11:73356800-73357000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:73356800-73357000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:73356800-73357000	Enhancers	Colon Smooth Muscle	Colon
48	chr11:73356800-73357000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
49	chr11:73356800-73357000	Bivalent Enhancer	NH-A	brain
50	chr11:73356800-73357200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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