Variant report

Variant	rs28578965
Chromosome Location	chr9:101015519-101015520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100962685..100965590-chr9:101014024..101016888,3	K562	blood:
2	chr9:100745090..100746942-chr9:101014665..101017073,2	MCF-7	breast:
3	chr9:100744384..100747791-chr9:101014978..101019057,4	MCF-7	breast:
4	chr9:100979926..100982589-chr9:101013541..101016209,2	MCF-7	breast:
5	chr9:101010838..101012752-chr9:101014329..101016410,2	MCF-7	breast:
6	chr9:100683079..100687048-chr9:101015405..101020638,4	K562	blood:
7	chr9:100951866..100957184-chr9:101014234..101020511,10	K562	blood:
8	chr9:100954775..100957184-chr9:101014893..101018488,3	K562	blood:
9	chr9:100683079..100686023-chr9:101015405..101017576,2	K562	blood:
10	chr9:101011351..101016361-chr9:101016435..101019100,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000095383	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000106789	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10046819	1.00[ASN][1000 genomes]
rs10114211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123613	0.87[AFR][1000 genomes]
rs10217245	1.00[ASN][1000 genomes]
rs10217458	1.00[ASN][1000 genomes]
rs10441752	1.00[ASN][1000 genomes]
rs10818608	1.00[ASN][1000 genomes]
rs10985425	1.00[ASN][1000 genomes]
rs10985528	1.00[ASN][1000 genomes]
rs10985545	1.00[ASN][1000 genomes]
rs10985570	1.00[ASN][1000 genomes]
rs10985573	1.00[ASN][1000 genomes]
rs10985578	1.00[ASN][1000 genomes]
rs10985730	1.00[ASN][1000 genomes]
rs12339078	1.00[ASN][1000 genomes]
rs12342843	1.00[ASN][1000 genomes]
rs12342968	1.00[ASN][1000 genomes]
rs12347046	1.00[ASN][1000 genomes]
rs12351571	1.00[ASN][1000 genomes]
rs12352986	1.00[ASN][1000 genomes]
rs16914199	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16914443	1.00[ASN][1000 genomes]
rs28524952	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28660099	0.87[AFR][1000 genomes]
rs28680284	0.87[AFR][1000 genomes]
rs28814444	0.95[EUR][1000 genomes]
rs34562398	1.00[ASN][1000 genomes]
rs36074616	1.00[ASN][1000 genomes]
rs41273923	1.00[ASN][1000 genomes]
rs41273925	1.00[ASN][1000 genomes]
rs41283618	1.00[ASN][1000 genomes]
rs4742725	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55974101	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57611604	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58371820	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59519660	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61201457	1.00[ASN][1000 genomes]
rs73490714	1.00[ASN][1000 genomes]
rs73490718	1.00[ASN][1000 genomes]
rs73490720	1.00[ASN][1000 genomes]
rs73490723	1.00[ASN][1000 genomes]
rs73490727	1.00[ASN][1000 genomes]
rs73490728	1.00[ASN][1000 genomes]
rs9299277	1.00[ASN][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	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100989600-101016000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:100992200-101016000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr9:100995000-101016600	Weak transcription	Brain Angular Gyrus	brain
4	chr9:100996000-101016000	Weak transcription	Pancreas	Pancrea
5	chr9:100996200-101017200	Weak transcription	Ovary	ovary
6	chr9:101004200-101015800	Weak transcription	Brain Hippocampus Middle	brain
7	chr9:101004200-101017200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:101005200-101017200	Weak transcription	Brain Germinal Matrix	brain
9	chr9:101006600-101016600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:101006800-101016800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:101009000-101017200	Weak transcription	Aorta	Aorta
12	chr9:101009200-101015800	Weak transcription	Stomach Mucosa	stomach
13	chr9:101009200-101016600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:101010200-101015600	Enhancers	NHDF-Ad	bronchial
15	chr9:101010200-101016600	Enhancers	Primary B cells from cord blood	blood
16	chr9:101010600-101017200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr9:101011000-101016600	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:101011600-101015800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:101011600-101015800	Weak transcription	Fetal Thymus	thymus
20	chr9:101011600-101016600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr9:101011600-101017200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:101011600-101017200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:101011800-101015600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:101011800-101016000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:101011800-101016000	Weak transcription	Adipose Nuclei	Adipose
26	chr9:101011800-101016400	Weak transcription	Primary T cells from cord blood	blood
27	chr9:101011800-101016600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:101011800-101017200	Weak transcription	Left Ventricle	heart
29	chr9:101012400-101015600	Enhancers	NH-A	brain
30	chr9:101012600-101016600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr9:101012800-101016600	Weak transcription	Fetal Lung	lung
32	chr9:101013000-101016800	Weak transcription	Right Ventricle	heart
33	chr9:101013000-101016800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr9:101013000-101017000	Weak transcription	Right Atrium	heart
35	chr9:101013000-101017200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:101013200-101016600	Weak transcription	HepG2	liver
37	chr9:101013200-101016800	Weak transcription	Fetal Stomach	stomach
38	chr9:101013400-101015800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:101013400-101016600	Weak transcription	Liver	Liver
40	chr9:101013600-101016200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:101014000-101015600	Enhancers	Colonic Mucosa	Colon
42	chr9:101014000-101015800	Enhancers	Esophagus	oesophagus
43	chr9:101014000-101015800	Genic enhancers	Spleen	Spleen
44	chr9:101014000-101016000	Weak transcription	Brain Substantia Nigra	brain
45	chr9:101014000-101016200	Transcr. at gene 5' and 3'	NHEK	skin
46	chr9:101014000-101016600	Transcr. at gene 5' and 3'	HSMM	muscle
47	chr9:101014000-101017400	Flanking Active TSS	Hela-S3	cervix
48	chr9:101014200-101016600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr9:101014200-101016800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:101014200-101017200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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