Variant report

Variant	rs11039202
Chromosome Location	chr11:47382426-47382427
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47376739..47379188-chr11:47381497..47383536,3	MCF-7	breast:
2	chr11:47381478..47383023-chr11:47384952..47387041,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1057233	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10734557	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10742803	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10769258	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10769262	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838698	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838699	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838704	0.84[EUR][1000 genomes]
rs10838706	0.85[EUR][1000 genomes]
rs11039195	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039199	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11039200	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11039203	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039212	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039219	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11600581	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11601603	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11605672	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11607981	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12146565	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12802273	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12803525	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1317164	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1542321	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2053979	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2053980	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2071304	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2084946	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2293577	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2293578	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2293580	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2856661	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35496532	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35996350	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3740686	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3781624	0.82[EUR][1000 genomes]
rs3781625	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3781626	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4752827	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752987	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752990	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4752993	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752994	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4752999	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4992357	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55677087	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55876153	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55927797	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56030824	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58965622	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60075622	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6485753	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67116452	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67472071	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7105851	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7107726	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs755553	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs755554	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs755555	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7924485	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7928163	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7928419	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7937331	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7940536	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs896816	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs935914	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	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
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11039202	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs11039202	C1QTNF4	cis	Muscle Skeletal	GTEx
rs11039202	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs11039202	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47377200-47386600	Weak transcription	Right Atrium	heart
2	chr11:47377200-47391400	Weak transcription	Psoas Muscle	Psoas
3	chr11:47377200-47397800	Weak transcription	Fetal Muscle Leg	muscle
4	chr11:47377600-47396800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr11:47377600-47397600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr11:47377600-47397800	Weak transcription	Brain Substantia Nigra	brain
7	chr11:47377800-47382600	Weak transcription	Fetal Heart	heart
8	chr11:47377800-47382800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:47378800-47393400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:47380000-47397800	Weak transcription	Esophagus	oesophagus
11	chr11:47380200-47383600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:47380200-47395200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr11:47380200-47396600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:47380200-47397200	Weak transcription	Brain Anterior Caudate	brain
15	chr11:47380200-47397800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr11:47380400-47382800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:47380400-47382800	Weak transcription	GM12878-XiMat	blood
18	chr11:47380400-47383600	Enhancers	Dnd41	blood
19	chr11:47380400-47389000	Genic enhancers	Primary monocytes fromperipheralblood	blood
20	chr11:47380400-47397000	Weak transcription	Lung	lung
21	chr11:47380800-47382800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr11:47380800-47383000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr11:47380800-47383200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:47381000-47383000	Enhancers	Fetal Thymus	thymus
25	chr11:47381000-47395400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:47381200-47384800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:47381400-47382800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr11:47381600-47382600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:47381600-47382800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr11:47381600-47382800	Weak transcription	Placenta	Placenta
31	chr11:47381600-47396800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr11:47381800-47382800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:47381800-47385400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr11:47382000-47382800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr11:47382000-47383400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:47382000-47383600	Strong transcription	Spleen	Spleen
37	chr11:47382000-47395200	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:47382200-47382600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
39	chr11:47382200-47382800	Genic enhancers	Monocytes-CD14+_RO01746	blood
40	chr11:47382200-47383000	Weak transcription	Primary B cells from cord blood	blood
41	chr11:47382200-47383000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr11:47382200-47395200	Weak transcription	Fetal Intestine Small	intestine

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