Variant report

Variant	rs1729297
Chromosome Location	chr11:47946162-47946163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47936350..47939236-chr11:47942544..47946300,3	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10769307	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838790	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039473	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11039480	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12270546	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12272781	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12273589	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1227997	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1227999	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1228000	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1228002	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1228004	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1228008	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228018	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1228019	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228020	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228021	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228022	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1228023	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12290628	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12294218	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12295364	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1681604	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1681627	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1681631	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1681637	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1729281	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1729294	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2626567	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2697810	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2930188	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2930189	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2930192	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2930195	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2950888	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4752883	0.87[EUR][1000 genomes]
rs4752886	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6485797	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7104376	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7111419	0.86[ASN][1000 genomes]
rs7113640	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7116080	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7117644	0.88[EUR][1000 genomes]
rs7119280	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73462871	0.86[ASN][1000 genomes]
rs73462874	0.86[ASN][1000 genomes]
rs73462875	0.86[ASN][1000 genomes]
rs7928153	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7932759	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7941441	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1729297	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47934000-47946600	Enhancers	Primary B cells from cord blood	blood
2	chr11:47934400-47947200	Enhancers	Primary B cells from peripheral blood	blood
3	chr11:47937400-47949800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:47939600-47946600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr11:47940200-47950000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:47941400-47949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:47942200-47946400	Enhancers	Fetal Thymus	thymus
8	chr11:47942400-47946200	Enhancers	Thymus	Thymus
9	chr11:47943000-47949600	Weak transcription	Primary T cells from cord blood	blood
10	chr11:47943200-47949800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr11:47943200-47949800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:47943200-47950000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:47944000-47946400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:47944200-47946200	Enhancers	Lung	lung
15	chr11:47944200-47947200	Enhancers	Placenta	Placenta
16	chr11:47944400-47949800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:47944600-47946200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:47944800-47946200	Enhancers	NHDF-Ad	bronchial
19	chr11:47944800-47946400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr11:47944800-47946400	Enhancers	Osteobl	bone
21	chr11:47944800-47946600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr11:47945000-47946200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:47945000-47946200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr11:47945000-47946200	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr11:47945000-47946400	Enhancers	NHLF	lung
26	chr11:47945200-47946200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:47945200-47946200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:47945200-47946200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:47945200-47946200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:47945200-47946200	Enhancers	Colon Smooth Muscle	Colon
31	chr11:47945200-47946200	Enhancers	Fetal Lung	lung
32	chr11:47945200-47946200	Enhancers	Fetal Stomach	stomach
33	chr11:47945200-47946200	Enhancers	Rectal Smooth Muscle	rectum
34	chr11:47945200-47946200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr11:47945200-47946200	Enhancers	GM12878-XiMat	blood
36	chr11:47945200-47946200	Enhancers	HSMMtube	muscle
37	chr11:47945200-47946200	Enhancers	HUVEC	blood vessel
38	chr11:47945200-47946400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:47945200-47946400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr11:47945200-47946400	Flanking Active TSS	Hela-S3	cervix
41	chr11:47945200-47946600	Enhancers	HSMM	muscle
42	chr11:47945400-47946200	Enhancers	Esophagus	oesophagus
43	chr11:47945400-47946200	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr11:47945400-47946200	Enhancers	NH-A	brain
45	chr11:47945400-47946400	Enhancers	Stomach Mucosa	stomach
46	chr11:47945600-47946200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr11:47945600-47946200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:47945600-47946200	Enhancers	Liver	Liver
49	chr11:47945600-47946200	Enhancers	Fetal Intestine Small	intestine
50	chr11:47945600-47946200	Enhancers	Gastric	stomach

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