Variant report

Variant	rs4752838
Chromosome Location	chr11:47466006-47466007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47465962-47466064	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47464955..47466544-chr11:47469002..47472026,3	K562	blood:
2	chr11:47290657..47292737-chr11:47464964..47467930,2	MCF-7	breast:
3	chr11:47461517..47466481-chr11:47469061..47471319,5	K562	blood:
4	chr11:47445759..47448729-chr11:47464943..47467214,2	K562	blood:
5	chr11:47458007..47459868-chr11:47463393..47467045,3	K562	blood:

No data

Variant related genes	Relation type
RNU6-1302P	TF binding region
RAPSN	TF binding region
ENSG00000165917	Chromatin interaction
ENSG00000165916	Chromatin interaction
ENSG00000110514	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10742803	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769262	0.81[EUR][1000 genomes]
rs10838704	0.90[ASN][1000 genomes]
rs10838706	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838724	0.88[ASN][1000 genomes]
rs11039219	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039238	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039255	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11039265	0.84[ASN][1000 genomes]
rs11600581	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11604680	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11605672	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12802273	0.81[EUR][1000 genomes]
rs1317149	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1317164	0.81[EUR][1000 genomes]
rs2053979	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2053980	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2293577	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293578	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2293580	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2868459	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34958982	0.88[ASN][1000 genomes]
rs35184771	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35496532	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35705029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781624	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3781625	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3781626	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3781627	0.90[ASN][1000 genomes]
rs4752832	0.82[ASN][1000 genomes]
rs4752845	0.89[ASN][1000 genomes]
rs4752993	0.81[EUR][1000 genomes]
rs4752994	0.81[EUR][1000 genomes]
rs4752999	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55927797	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60075622	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6485753	0.81[EUR][1000 genomes]
rs6485756	0.82[ASN][1000 genomes]
rs7106956	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107726	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7124681	0.91[ASN][1000 genomes]
rs755553	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs755554	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs755555	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7924485	0.82[EUR][1000 genomes]
rs7925389	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7937331	0.83[EUR][1000 genomes];0.89[ASN][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	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv975328	chr11:47446815-47471052	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4752838	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs4752838	C1QTNF4	cis	Muscle Skeletal	GTEx
rs4752838	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs4752838	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs4752838	SPI1	cis	multi-tissue	Pritchard

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:47453400-47469200	Weak transcription	Psoas Muscle	Psoas
3	chr11:47453400-47480000	Weak transcription	Thymus	Thymus
4	chr11:47456600-47468600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr11:47457400-47480200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:47457400-47480800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:47457400-47488400	Weak transcription	Gastric	stomach
8	chr11:47457800-47469000	Weak transcription	Spleen	Spleen
9	chr11:47459800-47466400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:47459800-47469400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:47459800-47470800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:47459800-47480600	Weak transcription	Fetal Intestine Small	intestine
13	chr11:47459800-47480800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:47460000-47470800	Weak transcription	Lung	lung
15	chr11:47460000-47475600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:47460600-47469200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:47461800-47480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:47463600-47469200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:47463600-47469200	Weak transcription	Placenta	Placenta
20	chr11:47463600-47469400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:47464000-47481000	Weak transcription	NHEK	skin
22	chr11:47464600-47466200	Enhancers	HepG2	liver
23	chr11:47464800-47468600	Weak transcription	HSMMtube	muscle
24	chr11:47465000-47480800	Weak transcription	Adipose Nuclei	Adipose
25	chr11:47465200-47467400	Weak transcription	HSMM	muscle
26	chr11:47465200-47467600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr11:47465200-47467800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr11:47465200-47469000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:47465200-47475600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:47465400-47466200	Strong transcription	Fetal Muscle Leg	muscle
31	chr11:47465400-47468600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:47465400-47470400	Weak transcription	Left Ventricle	heart
33	chr11:47465800-47480800	Weak transcription	Primary T cells from cord blood	blood
34	chr11:47466000-47471200	Weak transcription	Liver	Liver
35	chr11:47466000-47475600	Weak transcription	Fetal Thymus	thymus

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