Variant report

Variant	rs28851907
Chromosome Location	chr9:108232390-108232391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108231365..108233350-chr9:108238200..108241165,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1048215	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10491809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10816281	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10816283	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816285	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816286	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10816287	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816288	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816289	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10820804	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820811	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10820814	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10820815	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10978169	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10978172	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10978176	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10978177	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10978179	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10991659	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10991673	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10991677	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10991679	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11562356	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12336250	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12336844	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12337780	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12345599	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12352975	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1327352	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1327355	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1887367	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296750	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297023	0.80[ASN][1000 genomes]
rs2417625	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28542455	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3750500	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3793639	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3818598	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55798036	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7023302	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7023520	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7033138	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7033165	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7034149	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7037104	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7037141	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7037218	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7038407	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7047791	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72744263	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72744264	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7852541	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7854411	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7856617	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7857186	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs997319	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
5	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108211000-108248000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:108212200-108234800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
4	chr9:108220200-108243400	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:108220400-108237400	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:108220400-108252600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:108220600-108237000	Weak transcription	Pancreas	Pancrea
8	chr9:108220600-108237400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:108220800-108237000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:108220800-108237600	Weak transcription	Aorta	Aorta
11	chr9:108221000-108233200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:108221000-108235400	Weak transcription	Gastric	stomach
13	chr9:108221000-108236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:108221000-108237400	Weak transcription	Brain Substantia Nigra	brain
15	chr9:108221000-108257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:108221000-108257200	Weak transcription	Fetal Stomach	stomach
17	chr9:108221000-108266000	Weak transcription	NHEK	skin
18	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
19	chr9:108221200-108232800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:108221200-108235000	Weak transcription	Spleen	Spleen
21	chr9:108221800-108236600	Weak transcription	Small Intestine	intestine
22	chr9:108221800-108238200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr9:108222000-108237600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:108222200-108237400	Weak transcription	Psoas Muscle	Psoas
25	chr9:108222200-108259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:108222200-108277000	Weak transcription	Ovary	ovary
27	chr9:108222400-108236800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:108222400-108242200	Weak transcription	Brain Anterior Caudate	brain
29	chr9:108222400-108259000	Weak transcription	HSMMtube	muscle
30	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
31	chr9:108223200-108252600	Weak transcription	K562	blood
32	chr9:108223600-108255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:108224800-108244000	Weak transcription	Fetal Brain Male	brain
34	chr9:108225000-108237000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr9:108225000-108249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr9:108225800-108233600	Strong transcription	A549	lung
37	chr9:108226400-108232400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:108226400-108234800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:108226600-108233600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:108226600-108234000	Strong transcription	NHDF-Ad	bronchial
41	chr9:108226600-108235600	Strong transcription	HepG2	liver
42	chr9:108226800-108235400	Strong transcription	HSMM	muscle
43	chr9:108227000-108233600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:108227400-108232800	Weak transcription	GM12878-XiMat	blood
45	chr9:108227400-108271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:108227800-108232600	Weak transcription	Hela-S3	cervix
48	chr9:108227800-108239200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr9:108228000-108258800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr9:108228200-108235800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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