Variant report

Variant	rs10769264
Chromosome Location	chr11:47423340-47423341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47207092..47208885-chr11:47420633..47423542,2	K562	blood:
2	chr11:47420444..47424832-chr11:47425633..47430159,5	MCF-7	breast:
3	chr11:47397121..47400538-chr11:47420513..47424481,4	K562	blood:

Variant related genes	Relation type
ENSG00000165915	Chromatin interaction
ENSG00000066336	Chromatin interaction
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10437655	0.92[EUR][1000 genomes]
rs10742802	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742814	0.95[JPT][hapmap]
rs10769263	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838702	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838705	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838726	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10838732	0.95[JPT][hapmap]
rs11039221	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039244	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11039280	1.00[JPT][hapmap]
rs11606287	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs12292911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12361415	0.82[CHB][hapmap]
rs12577643	0.87[ASN][1000 genomes]
rs1377416	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1534576	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2203712	0.95[JPT][hapmap]
rs2242081	0.95[JPT][hapmap]
rs2278890	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2293576	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2293579	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35032070	0.87[EUR][1000 genomes]
rs3740689	0.83[CHB][hapmap]
rs3740699	0.84[JPT][hapmap]
rs3758675	0.83[EUR][1000 genomes]
rs3824869	0.89[CEU][hapmap]
rs4434960	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61897431	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6485758	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7103648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7104036	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7933019	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7947450	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7950696	0.95[JPT][hapmap]
rs874896	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs896817	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[YRI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
8	nsv541034	chr11:47404083-47440081	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10769264	C1QTNF4	cis	multi-tissue	Pritchard
rs10769264	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10769264		cis	Lymphoblastoid	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47420000-47423400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr11:47421200-47423400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:47422200-47423400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr11:47422200-47423600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:47422200-47428800	Weak transcription	NH-A	brain
6	chr11:47422400-47423400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:47422400-47423400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:47422400-47423600	Enhancers	Primary B cells from peripheral blood	blood
9	chr11:47422400-47423800	Enhancers	Primary hematopoietic stem cells	blood
10	chr11:47422400-47423800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr11:47422400-47428800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:47422400-47429000	Weak transcription	Fetal Brain Female	brain
13	chr11:47422600-47423400	Enhancers	K562	blood
14	chr11:47422600-47423600	Weak transcription	Gastric	stomach
15	chr11:47422600-47423800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:47422600-47424600	Weak transcription	HepG2	liver
17	chr11:47422600-47429000	Weak transcription	HSMMtube	muscle
18	chr11:47422800-47423600	Enhancers	Primary B cells from cord blood	blood
19	chr11:47422800-47423800	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:47422800-47424800	Weak transcription	Spleen	Spleen
21	chr11:47422800-47425000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr11:47422800-47428200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:47422800-47428200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:47422800-47428400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:47422800-47428400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:47422800-47428400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:47422800-47428400	Weak transcription	Fetal Muscle Leg	muscle
28	chr11:47422800-47428600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:47422800-47428800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:47422800-47428800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:47422800-47429000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:47422800-47429000	Weak transcription	Brain Angular Gyrus	brain
33	chr11:47423000-47423400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr11:47423000-47423600	Enhancers	GM12878-XiMat	blood
35	chr11:47423000-47428200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:47423000-47428400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr11:47423000-47428400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:47423000-47428400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:47423000-47428400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr11:47423000-47428400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:47423000-47428400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:47423000-47428400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:47423000-47428400	Weak transcription	Hela-S3	cervix
44	chr11:47423000-47428600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr11:47423000-47428600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:47423000-47428600	Weak transcription	Brain Substantia Nigra	brain
47	chr11:47423000-47428800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr11:47423000-47428800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:47423200-47423400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr11:47423200-47423600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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