Variant report

Variant	rs12339012
Chromosome Location	chr9:102615450-102615451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:102582575..102585075-chr9:102615014..102616883,2	K562	blood:
2	chr9:102614101..102615625-chr9:102620397..102622251,2	MCF-7	breast:
3	chr9:102605319..102608500-chr9:102612977..102616501,4	K562	blood:

Variant related genes	Relation type
ENSG00000119508	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12343669	0.84[ASW][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12344655	0.84[ASW][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7020565	0.92[ASW][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7032280	0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7035044	0.85[YRI][hapmap]
rs7036004	0.84[ASW][hapmap];0.92[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7039228	0.80[LWK][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7046311	0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7850043	0.85[YRI][hapmap]

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	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	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:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102591200-102618400	Weak transcription	Brain Angular Gyrus	brain
2	chr9:102591400-102616200	Weak transcription	Lung	lung
3	chr9:102592200-102618400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:102594200-102622000	Weak transcription	Brain Germinal Matrix	brain
5	chr9:102595400-102628200	Weak transcription	Fetal Brain Female	brain
6	chr9:102596200-102616400	Weak transcription	Fetal Brain Male	brain
7	chr9:102596200-102620400	Weak transcription	Fetal Heart	heart
8	chr9:102597200-102621800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:102601400-102620800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:102605400-102621800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:102607000-102617800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:102608600-102620400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:102609800-102627000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:102610400-102631200	Weak transcription	NHLF	lung
15	chr9:102610400-102644000	Weak transcription	Aorta	Aorta
16	chr9:102610600-102621600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:102610600-102621600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:102611400-102627000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr9:102611800-102628800	Weak transcription	Right Ventricle	heart
20	chr9:102612200-102618800	Weak transcription	Spleen	Spleen
21	chr9:102612200-102621400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:102612800-102628200	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:102613400-102626200	Weak transcription	Gastric	stomach
24	chr9:102613400-102628800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:102613800-102625200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:102614000-102615600	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr9:102614000-102621800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:102614400-102615600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:102614400-102626800	Weak transcription	Thymus	Thymus
30	chr9:102614400-102627600	Weak transcription	Primary T cells from cord blood	blood
31	chr9:102614800-102618400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr9:102615000-102615600	Weak transcription	Esophagus	oesophagus
33	chr9:102615000-102627600	Weak transcription	Psoas Muscle	Psoas
34	chr9:102615200-102617800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr9:102615200-102617800	Weak transcription	Left Ventricle	heart
36	chr9:102615200-102621600	Weak transcription	Ovary	ovary
37	chr9:102615400-102617400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:102615400-102617800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr9:102615400-102621200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:102615400-102625400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:102615400-102625800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:102615400-102626000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr9:102615400-102628600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr9:102615400-102644000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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