Variant report

Variant	rs11039265
Chromosome Location	chr11:47523214-47523215
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47522240..47523818-chr11:47530043..47531657,2	K562	blood:
2	chr11:47515511..47517710-chr11:47521817..47524345,2	MCF-7	breast:
3	chr11:47517168..47520094-chr11:47522959..47526818,3	K562	blood:
4	chr11:47521843..47524187-chr11:47526565..47529247,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10742803	0.80[ASN][1000 genomes]
rs10838724	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039238	0.84[ASN][1000 genomes]
rs11039255	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11600581	0.80[ASN][1000 genomes]
rs11604680	0.85[ASN][1000 genomes]
rs1317149	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2293577	0.80[ASN][1000 genomes]
rs2293578	0.80[ASN][1000 genomes]
rs2293580	0.80[ASN][1000 genomes]
rs2868459	0.85[ASN][1000 genomes]
rs34958982	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35184771	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35496532	0.81[ASN][1000 genomes]
rs35705029	0.84[ASN][1000 genomes]
rs3781624	0.81[ASN][1000 genomes]
rs3781626	0.81[ASN][1000 genomes]
rs4752838	0.84[ASN][1000 genomes]
rs4752845	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55927797	0.80[ASN][1000 genomes]
rs60075622	0.81[ASN][1000 genomes]
rs7106956	0.85[ASN][1000 genomes]
rs7124681	0.92[ASN][1000 genomes]
rs7925389	0.83[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	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
2	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
3	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv972949	chr11:47521522-47525037	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11039265	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs11039265	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs11039265	C1QTNF4	cis	Whole Blood	GTEx
rs11039265	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs11039265	C1QTNF4	cis	Muscle Skeletal	GTEx
rs11039265	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47507000-47528200	Weak transcription	Small Intestine	intestine
2	chr11:47508400-47530200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:47509000-47534400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:47509200-47530400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:47510200-47536800	Weak transcription	Fetal Kidney	kidney
6	chr11:47510800-47529800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:47511000-47525000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:47511200-47528600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr11:47513000-47525000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:47513400-47528400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:47515600-47528200	Weak transcription	NH-A	brain
12	chr11:47516800-47530200	Weak transcription	Colonic Mucosa	Colon
13	chr11:47517400-47523400	Strong transcription	NHEK	skin
14	chr11:47517600-47523800	Enhancers	Colon Smooth Muscle	Colon
15	chr11:47518600-47526200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:47519000-47529200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:47519200-47526600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:47519200-47527000	Strong transcription	Hela-S3	cervix
19	chr11:47519400-47523400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
20	chr11:47519600-47524800	Enhancers	Brain Anterior Caudate	brain
21	chr11:47520000-47525000	Weak transcription	Fetal Intestine Small	intestine
22	chr11:47520000-47528200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:47520400-47523400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr11:47520400-47524000	Strong transcription	HSMM	muscle
25	chr11:47520400-47526000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr11:47520400-47528800	Weak transcription	Thymus	Thymus
27	chr11:47520400-47529000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:47520800-47523400	Genic enhancers	Fetal Muscle Leg	muscle
29	chr11:47520800-47523600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:47521000-47523400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:47521000-47525000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr11:47521200-47527000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr11:47521400-47523600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr11:47521400-47525400	Weak transcription	Fetal Stomach	stomach
35	chr11:47521600-47523400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr11:47521600-47525400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:47521600-47526000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:47521600-47528600	Weak transcription	A549	lung
39	chr11:47521600-47529800	Weak transcription	Gastric	stomach
40	chr11:47521600-47530200	Weak transcription	Right Ventricle	heart
41	chr11:47521600-47531000	Weak transcription	Lung	lung
42	chr11:47521600-47534000	Weak transcription	Aorta	Aorta
43	chr11:47521600-47534400	Weak transcription	HUVEC	blood vessel
44	chr11:47521800-47523400	Enhancers	Liver	Liver
45	chr11:47521800-47524000	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr11:47521800-47527800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr11:47521800-47528000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:47521800-47528000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr11:47521800-47528000	Weak transcription	Ovary	ovary
50	chr11:47521800-47528000	Weak transcription	Stomach Mucosa	stomach

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