Variant report

Variant	rs11039244
Chromosome Location	chr11:47466442-47466443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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:

Variant related genes	Relation type
ENSG00000165916	Chromatin interaction
ENSG00000165917	Chromatin interaction
ENSG00000110514	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10742802	0.89[ASN][1000 genomes]
rs10742814	0.90[JPT][hapmap]
rs10769264	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10838702	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs10838703	0.92[CEU][hapmap]
rs10838705	0.87[ASN][1000 genomes]
rs10838709	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10838726	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs10838732	0.90[JPT][hapmap]
rs11039221	0.87[ASN][1000 genomes]
rs11039225	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11039280	0.94[JPT][hapmap]
rs11039290	0.88[CEU][hapmap]
rs12292911	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12361415	0.82[CHB][hapmap]
rs12577643	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1377416	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs1534576	0.84[CEU][hapmap];0.94[CHB][hapmap]
rs2203712	0.90[JPT][hapmap]
rs2242081	0.90[JPT][hapmap]
rs2293576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293579	0.88[ASN][1000 genomes]
rs3740689	0.83[CHB][hapmap]
rs4434960	0.89[ASN][1000 genomes]
rs61897431	0.86[ASN][1000 genomes]
rs6485758	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6485763	0.90[JPT][hapmap]
rs7103648	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7103835	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs7104036	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7120548	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7933019	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7947450	0.87[ASN][1000 genomes]
rs7950696	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs874896	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs896817	0.84[CEU][hapmap];0.88[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11039244		cis	Lymphoblastoid	GTEx
rs11039244	C1QTNF4	cis	multi-tissue	Pritchard
rs11039244	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 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	chr11:47459800-47469400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:47459800-47470800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:47459800-47480600	Weak transcription	Fetal Intestine Small	intestine
12	chr11:47459800-47480800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:47460000-47470800	Weak transcription	Lung	lung
14	chr11:47460000-47475600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:47460600-47469200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:47461800-47480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:47463600-47469200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:47463600-47469200	Weak transcription	Placenta	Placenta
19	chr11:47463600-47469400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:47464000-47481000	Weak transcription	NHEK	skin
21	chr11:47464800-47468600	Weak transcription	HSMMtube	muscle
22	chr11:47465000-47480800	Weak transcription	Adipose Nuclei	Adipose
23	chr11:47465200-47467400	Weak transcription	HSMM	muscle
24	chr11:47465200-47467600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr11:47465200-47467800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:47465200-47469000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:47465200-47475600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:47465400-47468600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:47465400-47470400	Weak transcription	Left Ventricle	heart
30	chr11:47465800-47480800	Weak transcription	Primary T cells from cord blood	blood
31	chr11:47466000-47471200	Weak transcription	Liver	Liver
32	chr11:47466000-47475600	Weak transcription	Fetal Thymus	thymus
33	chr11:47466200-47467400	Weak transcription	Fetal Muscle Leg	muscle
34	chr11:47466200-47469000	Weak transcription	HepG2	liver

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