Variant report

Variant	rs11039280
Chromosome Location	chr11:47558858-47558859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47556312..47559007-chr11:47559496..47562082,2	MCF-7	breast:
2	chr11:47557985..47562133-chr11:47565496..47569267,5	K562	blood:
3	chr11:47553494..47556204-chr11:47558570..47560706,2	MCF-7	breast:
4	chr11:47556325..47561893-chr11:47562676..47568878,7	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1056387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10742814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10742817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs10769264	1.00[JPT][hapmap]
rs10769288	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs10838709	1.00[JPT][hapmap]
rs10838725	0.85[ASN][1000 genomes]
rs10838726	1.00[JPT][hapmap]
rs10838732	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs10838740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10838746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11039225	1.00[JPT][hapmap]
rs11039244	0.94[JPT][hapmap]
rs11039329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11039332	0.94[JPT][hapmap]
rs11039345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap]
rs12226590	0.86[AMR][1000 genomes]
rs12285933	1.00[YRI][hapmap]
rs12286721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12292911	1.00[JPT][hapmap]
rs12785949	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1563821	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2203712	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2242081	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290851	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2293576	1.00[JPT][hapmap]
rs3740699	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3758655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs4539273	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4752860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6485758	1.00[JPT][hapmap]
rs6485763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7103648	1.00[JPT][hapmap]
rs7120548	1.00[JPT][hapmap]
rs7129797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7933019	1.00[JPT][hapmap]
rs7936948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7939420	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7950696	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11039280	FNBP4	cis	lesional skin	skin_eQTL
rs11039280		cis	Lymphoblastoid	GTEx
rs11039280	C1QTNF4	cis	multi-tissue	Pritchard
rs11039280	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47546000-47572400	Weak transcription	Fetal Intestine Large	intestine
2	chr11:47546200-47560400	Weak transcription	Esophagus	oesophagus
3	chr11:47546400-47560400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:47546400-47560800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr11:47546400-47561200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:47546400-47564200	Weak transcription	Thymus	Thymus
7	chr11:47546400-47573400	Weak transcription	Colonic Mucosa	Colon
8	chr11:47546400-47573600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:47546600-47561000	Weak transcription	Stomach Mucosa	stomach
10	chr11:47546800-47559000	Strong transcription	Fetal Intestine Small	intestine
11	chr11:47546800-47560200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr11:47547200-47559600	Weak transcription	HUVEC	blood vessel
13	chr11:47547400-47560400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:47547400-47560800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:47547800-47562000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:47548200-47560400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:47549000-47559400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:47550400-47559200	Weak transcription	NHEK	skin
19	chr11:47550600-47561000	Weak transcription	Placenta	Placenta
20	chr11:47551000-47563200	Enhancers	Fetal Brain Male	brain
21	chr11:47551200-47559000	Weak transcription	Psoas Muscle	Psoas
22	chr11:47552200-47560400	Weak transcription	HMEC	breast
23	chr11:47552600-47560800	Weak transcription	Pancreas	Pancrea
24	chr11:47553000-47573200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:47554200-47561400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr11:47554400-47559400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr11:47554400-47560200	Weak transcription	Brain Angular Gyrus	brain
28	chr11:47554400-47560400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:47554400-47561200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:47554400-47561600	Weak transcription	Fetal Kidney	kidney
31	chr11:47554400-47572400	Weak transcription	Aorta	Aorta
32	chr11:47554600-47559400	Weak transcription	Brain Germinal Matrix	brain
33	chr11:47554600-47559400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:47554600-47560400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr11:47554600-47560400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:47554600-47560400	Weak transcription	NHDF-Ad	bronchial
37	chr11:47554600-47561200	Weak transcription	HepG2	liver
38	chr11:47554800-47559600	Strong transcription	Hela-S3	cervix
39	chr11:47554800-47571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr11:47554800-47572400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:47555000-47559400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:47555000-47560200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr11:47555000-47560400	Weak transcription	Gastric	stomach
44	chr11:47555000-47560800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr11:47555200-47559800	Weak transcription	Brain Substantia Nigra	brain
46	chr11:47555200-47560400	Weak transcription	NH-A	brain
47	chr11:47555200-47561000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr11:47555400-47560400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr11:47555400-47560400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:47555400-47560400	Weak transcription	Brain Anterior Caudate	brain

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