Variant report

Variant	rs55651016
Chromosome Location	chr9:98613664-98613665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98584113..98586604-chr9:98610986..98613982,2	MCF-7	breast:
2	chr9:98613149..98614774-chr9:98637250..98638861,2	MCF-7	breast:
3	chr9:98611900..98615420-chr9:98615884..98619826,3	MCF-7	breast:
4	chr9:98600432..98602813-chr9:98612011..98614211,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12003772	0.92[ASN][1000 genomes]
rs12551596	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12551880	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12554182	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12555687	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1413178	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16910333	1.00[ASN][1000 genomes]
rs16910342	1.00[ASN][1000 genomes]
rs16910409	0.93[ASN][1000 genomes]
rs16910427	0.93[ASN][1000 genomes]
rs17303073	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17303324	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2297009	0.95[ASN][1000 genomes]
rs2423	0.93[ASN][1000 genomes]
rs3739755	0.98[ASN][1000 genomes]
rs3739756	0.92[ASN][1000 genomes]
rs4742763	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742769	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742801	0.95[ASN][1000 genomes]
rs4743327	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4743351	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743383	1.00[ASN][1000 genomes]
rs4743460	0.92[ASN][1000 genomes]
rs4743469	0.84[ASN][1000 genomes]
rs55770584	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55781050	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55797980	0.92[ASN][1000 genomes]
rs55881510	0.95[ASN][1000 genomes]
rs56063686	0.98[ASN][1000 genomes]
rs56070531	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56110216	0.95[ASN][1000 genomes]
rs56125887	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56372801	0.92[ASN][1000 genomes]
rs56403401	0.95[ASN][1000 genomes]
rs57096664	1.00[ASN][1000 genomes]
rs59046245	0.97[ASN][1000 genomes]
rs59189545	0.98[ASN][1000 genomes]
rs61036807	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61093440	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9721742	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9792431	0.92[ASN][1000 genomes]
rs9792684	0.92[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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 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	chr9:98596200-98616400	Weak transcription	Fetal Brain Female	brain
2	chr9:98596200-98619200	Weak transcription	Fetal Heart	heart
3	chr9:98596400-98619400	Weak transcription	Right Ventricle	heart
4	chr9:98599200-98614400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:98602000-98632800	Weak transcription	Left Ventricle	heart
6	chr9:98602000-98636000	Weak transcription	Lung	lung
7	chr9:98602400-98619400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:98602600-98618800	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:98602600-98619400	Weak transcription	Psoas Muscle	Psoas
10	chr9:98602600-98620200	Weak transcription	Small Intestine	intestine
11	chr9:98602800-98614400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:98602800-98619000	Weak transcription	Ovary	ovary
13	chr9:98604400-98621200	Weak transcription	Primary T cells from cord blood	blood
14	chr9:98607400-98621600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr9:98608000-98614200	Weak transcription	NHLF	lung
16	chr9:98608200-98614400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:98608400-98614200	Weak transcription	Brain Substantia Nigra	brain
18	chr9:98608600-98614200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:98609000-98614200	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:98609000-98614800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr9:98609000-98615600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:98609000-98616600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:98609000-98617200	Weak transcription	Spleen	Spleen
24	chr9:98609000-98619400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:98609800-98614200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:98610200-98614000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:98610200-98636200	Weak transcription	Brain Germinal Matrix	brain
28	chr9:98610200-98636800	Weak transcription	Gastric	stomach
29	chr9:98610400-98618800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:98610600-98614000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:98610600-98614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:98610600-98616400	Weak transcription	Fetal Stomach	stomach
33	chr9:98610600-98618200	Weak transcription	Thymus	Thymus
34	chr9:98610600-98618800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:98610600-98619400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:98610800-98614400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:98610800-98614400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr9:98611000-98616000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:98611200-98620200	Weak transcription	Primary B cells from cord blood	blood
40	chr9:98611200-98620400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:98611400-98619200	Weak transcription	Fetal Intestine Small	intestine
42	chr9:98611800-98614000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:98611800-98614400	Weak transcription	Fetal Lung	lung
44	chr9:98611800-98614800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:98612200-98613800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:98612400-98615200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr9:98613400-98632800	Weak transcription	Rectal Mucosa Donor 29	rectum

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