Variant report

Variant	rs7039228
Chromosome Location	chr9:102609639-102609640
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102608148..102609729-chr9:102667494..102669204,2	MCF-7	breast:
2	chr9:102609492..102611847-chr9:102667260..102669320,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136874	Chromatin interaction
ENSG00000255145	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12339012	0.80[LWK][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12343669	0.85[ASW][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12344655	0.85[ASW][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7020565	0.85[ASW][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7032280	0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7036004	0.85[ASW][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7046311	0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv528025	chr9:102540386-102613672	Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102587000-102613800	Weak transcription	Hela-S3	cervix
2	chr9:102590600-102611200	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr9:102591200-102618400	Weak transcription	Brain Angular Gyrus	brain
4	chr9:102591400-102616200	Weak transcription	Lung	lung
5	chr9:102592200-102618400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:102594200-102613000	Weak transcription	Primary T cells from cord blood	blood
7	chr9:102594200-102622000	Weak transcription	Brain Germinal Matrix	brain
8	chr9:102595400-102628200	Weak transcription	Fetal Brain Female	brain
9	chr9:102596200-102616400	Weak transcription	Fetal Brain Male	brain
10	chr9:102596200-102620400	Weak transcription	Fetal Heart	heart
11	chr9:102597200-102609800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:102597200-102621800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:102597800-102611000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr9:102600600-102613000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:102601400-102620800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:102604200-102612000	Weak transcription	Fetal Stomach	stomach
17	chr9:102605400-102621800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:102606000-102613000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:102606000-102613200	Weak transcription	Fetal Thymus	thymus
20	chr9:102606800-102615200	Strong transcription	Left Ventricle	heart
21	chr9:102607000-102615400	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:102607000-102617800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:102607400-102612200	Weak transcription	Gastric	stomach
24	chr9:102607800-102609800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:102608000-102612600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:102608200-102610200	Strong transcription	Colon Smooth Muscle	Colon
27	chr9:102608400-102609800	Weak transcription	NHLF	lung
28	chr9:102608400-102611200	Weak transcription	Pancreas	Pancrea
29	chr9:102608600-102614400	Weak transcription	Psoas Muscle	Psoas
30	chr9:102608600-102620400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:102608800-102610600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:102608800-102614000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:102609000-102611600	Weak transcription	Small Intestine	intestine
34	chr9:102609200-102610400	Strong transcription	Aorta	Aorta
35	chr9:102609200-102611400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr9:102609200-102611800	Strong transcription	Right Ventricle	heart
37	chr9:102609400-102609800	Strong transcription	Ovary	ovary
38	chr9:102609400-102610000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr9:102609400-102610600	Enhancers	Stomach Mucosa	stomach
40	chr9:102609400-102613000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:102609400-102613800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr9:102609600-102610200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:102609600-102610400	Strong transcription	Thymus	Thymus
44	chr9:102609600-102610600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:102609600-102612400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:102609600-102615400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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