Variant report

Variant	rs11099669
Chromosome Location	chr4:148689511-148689512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148649361..148653898-chr4:148687606..148694872,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071205	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10027921	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs1119887	0.86[JPT][hapmap]
rs11729081	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11944579	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs12502667	0.86[AMR][1000 genomes]
rs12640660	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12645249	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12648074	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12650280	0.87[AMR][1000 genomes]
rs13116955	0.87[AMR][1000 genomes]
rs13134018	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13136202	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13136624	0.80[AFR][1000 genomes]
rs13136858	0.81[AFR][1000 genomes]
rs1604785	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs17023770	0.84[EUR][1000 genomes]
rs17023844	0.86[JPT][hapmap]
rs2055551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2118036	0.83[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs2134706	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs2164527	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4835448	0.84[AMR][1000 genomes]
rs4835456	0.85[CHB][hapmap]
rs62330668	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6535556	1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs6535558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6535559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6535560	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6535561	0.82[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6818043	0.84[EUR][1000 genomes]
rs6822971	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6836509	0.86[AMR][1000 genomes]
rs6839987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6840039	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6845560	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7673234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673606	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9332471	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs964170	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[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	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking 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	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880242	chr4:148659137-148727355	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148670200-148693200	Weak transcription	Esophagus	oesophagus
2	chr4:148678000-148693200	Weak transcription	Adipose Nuclei	Adipose
3	chr4:148679200-148693000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:148679200-148693000	Weak transcription	Aorta	Aorta
5	chr4:148679200-148696400	Weak transcription	Lung	lung
6	chr4:148682200-148693000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:148682400-148692400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:148684200-148691800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:148684400-148693600	Weak transcription	Fetal Kidney	kidney
10	chr4:148685200-148692200	Weak transcription	Right Atrium	heart
11	chr4:148685600-148691200	Weak transcription	Psoas Muscle	Psoas
12	chr4:148686000-148693000	Weak transcription	Ovary	ovary
13	chr4:148687000-148692000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:148687200-148696400	Weak transcription	Right Ventricle	heart
15	chr4:148687400-148691800	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:148688200-148689600	Enhancers	Left Ventricle	heart
17	chr4:148688600-148689800	Enhancers	Primary hematopoietic stem cells	blood
18	chr4:148688600-148689800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:148688600-148691400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:148688800-148689600	Enhancers	Colon Smooth Muscle	Colon
21	chr4:148688800-148689600	Enhancers	Rectal Smooth Muscle	rectum
22	chr4:148688800-148689800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr4:148688800-148689800	Enhancers	Stomach Mucosa	stomach
24	chr4:148688800-148690000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:148688800-148690200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:148688800-148690200	Enhancers	HSMM	muscle
27	chr4:148688800-148690400	Enhancers	GM12878-XiMat	blood
28	chr4:148688800-148690400	Enhancers	HMEC	breast
29	chr4:148688800-148690600	Enhancers	NH-A	brain
30	chr4:148688800-148690600	Enhancers	NHDF-Ad	bronchial
31	chr4:148688800-148691000	Enhancers	Osteobl	bone
32	chr4:148688800-148693400	Enhancers	HUVEC	blood vessel
33	chr4:148689000-148689600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:148689000-148689600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:148689000-148689600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:148689000-148689600	Enhancers	A549	lung
37	chr4:148689000-148689600	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr4:148689000-148689800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:148689000-148690000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:148689000-148690000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr4:148689000-148693200	Enhancers	NHEK	skin
42	chr4:148689200-148689600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr4:148689200-148689600	Enhancers	Gastric	stomach
44	chr4:148689200-148689600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr4:148689200-148689600	Enhancers	HSMMtube	muscle
46	chr4:148689200-148689600	Enhancers	NHLF	lung
47	chr4:148689200-148689800	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr4:148689200-148689800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:148689200-148691000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:148689400-148689600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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