Variant report

Variant	rs2773358
Chromosome Location	chr9:100356741-100356742
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	chr9:100355062..100357246-chr9:100361025..100362574,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1962592	0.80[EUR][1000 genomes]
rs2149984	0.90[EUR][1000 genomes]
rs2245694	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254733	0.91[EUR][1000 genomes]
rs2668795	0.81[CHD][hapmap]
rs2668797	0.86[CHD][hapmap]
rs2773343	0.82[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2773344	0.91[CEU][hapmap];0.99[EUR][1000 genomes]
rs2773349	0.94[EUR][1000 genomes]
rs2773350	0.92[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2773354	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs2805774	0.92[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2805783	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805785	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805786	1.00[EUR][1000 genomes]
rs2805787	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805788	1.00[EUR][1000 genomes]
rs2805792	0.96[EUR][1000 genomes]
rs2805793	0.91[EUR][1000 genomes]
rs2805802	0.83[EUR][1000 genomes]
rs2805804	0.80[EUR][1000 genomes]
rs2805831	0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs2808669	0.80[EUR][1000 genomes]
rs2808676	0.80[EUR][1000 genomes]
rs932916	0.90[EUR][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	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100333600-100361800	Weak transcription	Gastric	stomach
2	chr9:100336200-100360000	Weak transcription	Brain Substantia Nigra	brain
3	chr9:100338200-100356800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:100338400-100361600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:100338600-100360800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr9:100341200-100358400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:100346200-100360800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:100348800-100384000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:100350400-100361800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:100350600-100360800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:100351200-100361800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:100353000-100362800	Weak transcription	Esophagus	oesophagus
13	chr9:100353200-100362200	Enhancers	Fetal Brain Male	brain
14	chr9:100353200-100363200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr9:100353400-100359200	Strong transcription	K562	blood
16	chr9:100353600-100358600	Enhancers	Fetal Heart	heart
17	chr9:100354000-100360800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:100354000-100360800	Weak transcription	Lung	lung
19	chr9:100354200-100360600	Weak transcription	GM12878-XiMat	blood
20	chr9:100354800-100357400	Enhancers	Fetal Muscle Leg	muscle
21	chr9:100354800-100363000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:100355000-100360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:100355000-100360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:100355000-100360800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr9:100355400-100356800	Genic enhancers	Stomach Smooth Muscle	stomach
26	chr9:100355400-100357000	Enhancers	Psoas Muscle	Psoas
27	chr9:100355400-100360800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr9:100355600-100356800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr9:100355600-100357000	Enhancers	Left Ventricle	heart
30	chr9:100355600-100357400	Enhancers	Rectal Smooth Muscle	rectum
31	chr9:100355600-100357800	Enhancers	Colon Smooth Muscle	Colon
32	chr9:100355600-100359200	Weak transcription	Brain Germinal Matrix	brain
33	chr9:100355800-100357000	Enhancers	Right Ventricle	heart
34	chr9:100356000-100357000	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr9:100356000-100357000	Enhancers	Right Atrium	heart
36	chr9:100356000-100357400	Enhancers	Brain Cingulate Gyrus	brain
37	chr9:100356200-100357200	Genic enhancers	Aorta	Aorta
38	chr9:100356200-100357200	Enhancers	Fetal Muscle Trunk	muscle
39	chr9:100356200-100357800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr9:100356400-100357400	Enhancers	HSMMtube	muscle
41	chr9:100356400-100358800	Enhancers	Fetal Brain Female	brain
42	chr9:100356600-100357000	Enhancers	HSMM	muscle
43	chr9:100356600-100357200	Strong transcription	Ovary	ovary
44	chr9:100356600-100357200	Enhancers	Pancreas	Pancrea
45	chr9:100356600-100357400	Enhancers	Brain Angular Gyrus	brain
46	chr9:100356600-100357600	Enhancers	Brain Anterior Caudate	brain
47	chr9:100356600-100361400	Enhancers	Brain Hippocampus Middle	brain

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