Variant report

Variant	rs28431078
Chromosome Location	chr9:5908326-5908327
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	chr9:5894261..5896922-chr9:5907318..5910115,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10116214	1.00[EUR][1000 genomes]
rs10125832	1.00[EUR][1000 genomes]
rs10975350	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975351	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975362	1.00[EUR][1000 genomes]
rs10975363	1.00[EUR][1000 genomes]
rs10975364	1.00[EUR][1000 genomes]
rs10975367	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10975372	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10975377	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11506678	1.00[EUR][1000 genomes]
rs11793956	1.00[ASN][1000 genomes]
rs12337300	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337445	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337790	1.00[EUR][1000 genomes]
rs12339713	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12339886	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12339889	1.00[EUR][1000 genomes]
rs12340153	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340531	1.00[EUR][1000 genomes]
rs12341021	1.00[EUR][1000 genomes]
rs12342166	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343325	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345849	1.00[EUR][1000 genomes]
rs12351533	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411949	1.00[EUR][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs57154492	1.00[EUR][1000 genomes]
rs58291302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60037728	1.00[EUR][1000 genomes]
rs7022080	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029847	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73383109	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73383113	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73383114	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73383144	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73385128	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73389036	1.00[EUR][1000 genomes]
rs73389044	1.00[EUR][1000 genomes]
rs73397307	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73397376	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73399307	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73639554	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73639568	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854980	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858084	1.00[EUR][1000 genomes]
rs7858846	1.00[EUR][1000 genomes]
rs7874032	1.00[ASN][1000 genomes]
rs7875607	1.00[EUR][1000 genomes]
rs9299025	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5840400-5921600	Weak transcription	Right Ventricle	heart
2	chr9:5859200-5919800	Weak transcription	Fetal Brain Female	brain
3	chr9:5871000-5920000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:5884600-5910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:5886800-5920400	Weak transcription	GM12878-XiMat	blood
6	chr9:5886800-5920600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr9:5886800-5922000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:5887000-5921600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr9:5892600-5921600	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:5893000-5920000	Weak transcription	Thymus	Thymus
11	chr9:5894000-5910400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:5894400-5920400	Weak transcription	NH-A	brain
13	chr9:5894600-5910400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:5894600-5919800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:5895000-5908600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:5895800-5910400	Weak transcription	NHDF-Ad	bronchial
17	chr9:5896000-5921600	Weak transcription	Lung	lung
18	chr9:5896200-5920200	Weak transcription	Psoas Muscle	Psoas
19	chr9:5896200-5920800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:5896200-5921200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:5896400-5919800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:5896400-5921800	Weak transcription	Brain Angular Gyrus	brain
23	chr9:5896600-5919600	Weak transcription	Brain Anterior Caudate	brain
24	chr9:5896600-5919600	Weak transcription	Brain Substantia Nigra	brain
25	chr9:5896800-5919800	Weak transcription	Fetal Lung	lung
26	chr9:5896800-5920400	Weak transcription	Fetal Thymus	thymus
27	chr9:5897000-5921600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:5897400-5919800	Weak transcription	Placenta	Placenta
29	chr9:5897400-5922200	Weak transcription	Pancreas	Pancrea
30	chr9:5897600-5920000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:5897600-5920200	Weak transcription	HSMMtube	muscle
32	chr9:5897600-5921400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr9:5897600-5921800	Weak transcription	Spleen	Spleen
34	chr9:5897800-5919600	Weak transcription	Brain Hippocampus Middle	brain
35	chr9:5897800-5921800	Weak transcription	Gastric	stomach
36	chr9:5898000-5909800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:5898000-5919800	Weak transcription	Brain Germinal Matrix	brain
38	chr9:5898000-5920400	Weak transcription	Aorta	Aorta
39	chr9:5898000-5921800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr9:5898400-5921200	Weak transcription	Colonic Mucosa	Colon
41	chr9:5898400-5947200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr9:5898800-5920400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr9:5898800-5921800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:5899000-5920400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:5899200-5920000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr9:5899400-5919800	Weak transcription	Left Ventricle	heart
47	chr9:5899400-5923000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:5899800-5908400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr9:5900000-5910400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:5900000-5920400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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