Variant report

Variant	rs56125887
Chromosome Location	chr9:98585543-98585544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98584403..98586297-chr9:98637755..98640000,3	MCF-7	breast:
2	chr9:98583596..98587083-chr9:98587311..98591492,4	MCF-7	breast:
3	chr9:98569719..98571881-chr9:98585000..98587559,2	MCF-7	breast:
4	chr9:98571797..98574683-chr9:98583300..98586661,3	MCF-7	breast:
5	chr9:98584113..98586604-chr9:98610986..98613982,2	MCF-7	breast:
6	chr9:98578285..98580022-chr9:98583507..98586457,2	MCF-7	breast:
7	chr9:98583856..98586047-chr9:98617880..98619976,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12003772	0.88[ASN][1000 genomes]
rs12551596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12551880	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12554182	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12555687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910333	0.97[ASN][1000 genomes]
rs16910342	0.97[ASN][1000 genomes]
rs16910409	0.90[ASN][1000 genomes]
rs16910427	0.90[ASN][1000 genomes]
rs17303073	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17303324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297009	0.91[ASN][1000 genomes]
rs2423	0.90[ASN][1000 genomes]
rs3739755	0.95[ASN][1000 genomes]
rs3739756	0.88[ASN][1000 genomes]
rs4742763	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742769	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742801	0.91[ASN][1000 genomes]
rs4743327	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743351	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743383	0.97[ASN][1000 genomes]
rs4743460	0.88[ASN][1000 genomes]
rs4743469	0.81[ASN][1000 genomes]
rs55651016	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55770584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55781050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797980	0.88[ASN][1000 genomes]
rs55881510	0.91[ASN][1000 genomes]
rs56063686	0.95[ASN][1000 genomes]
rs56070531	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56110216	0.91[ASN][1000 genomes]
rs56372801	0.88[ASN][1000 genomes]
rs56403401	0.91[ASN][1000 genomes]
rs57096664	0.97[ASN][1000 genomes]
rs59046245	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59189545	0.95[ASN][1000 genomes]
rs61036807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61093440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9721742	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9792431	0.88[ASN][1000 genomes]
rs9792684	0.88[ASN][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	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

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98570400-98585800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:98570400-98589200	Weak transcription	Left Ventricle	heart
3	chr9:98570400-98589200	Weak transcription	Right Ventricle	heart
4	chr9:98570400-98593200	Weak transcription	Gastric	stomach
5	chr9:98570400-98593800	Weak transcription	Right Atrium	heart
6	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:98576000-98596000	Weak transcription	Aorta	Aorta
8	chr9:98577600-98585600	Weak transcription	Pancreas	Pancrea
9	chr9:98581800-98593800	Weak transcription	Fetal Intestine Small	intestine
10	chr9:98582400-98585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:98582600-98586000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr9:98583800-98586600	Enhancers	Placenta Amnion	Placenta Amnion
13	chr9:98584200-98585800	Enhancers	Ovary	ovary
14	chr9:98584400-98586000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:98584400-98586000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr9:98584400-98586200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:98584400-98586200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:98584600-98585800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:98584600-98585800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:98584600-98585800	Enhancers	A549	lung
21	chr9:98584600-98585800	Enhancers	Osteobl	bone
22	chr9:98584600-98586000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:98584600-98586000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:98584600-98586000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:98584600-98586000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:98584600-98586000	Flanking Active TSS	GM12878-XiMat	blood
27	chr9:98584600-98586000	Enhancers	NH-A	brain
28	chr9:98584800-98585600	Enhancers	NHDF-Ad	bronchial
29	chr9:98584800-98585800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:98584800-98585800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:98584800-98585800	Enhancers	Placenta	Placenta
32	chr9:98584800-98585800	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr9:98584800-98585800	Enhancers	Stomach Smooth Muscle	stomach
34	chr9:98584800-98585800	Enhancers	HSMM	muscle
35	chr9:98584800-98585800	Enhancers	HSMMtube	muscle
36	chr9:98584800-98585800	Enhancers	NHEK	skin
37	chr9:98584800-98586000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:98584800-98586000	Flanking Active TSS	Hela-S3	cervix
39	chr9:98584800-98586200	Enhancers	HUVEC	blood vessel
40	chr9:98585000-98585600	Enhancers	HMEC	breast
41	chr9:98585000-98585800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:98585000-98585800	Enhancers	Duodenum Mucosa	Duodenum
43	chr9:98585000-98585800	Enhancers	Fetal Stomach	stomach
44	chr9:98585000-98585800	Enhancers	Fetal Thymus	thymus
45	chr9:98585000-98586000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr9:98585200-98585600	Enhancers	NHLF	lung
47	chr9:98585200-98585800	Enhancers	Esophagus	oesophagus
48	chr9:98585200-98586200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr9:98585200-98593600	Weak transcription	Spleen	Spleen
50	chr9:98585400-98585600	Enhancers	Thymus	Thymus

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