Variant report

Variant	rs9409805
Chromosome Location	chr9:97512757-97512758
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	chr9:97510928..97513839-chr9:97515556..97518922,4	MCF-7	breast:

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10217441	0.85[EUR][1000 genomes]
rs10732407	0.85[EUR][1000 genomes]
rs10733756	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10739988	0.85[EUR][1000 genomes]
rs10739990	0.85[EUR][1000 genomes]
rs10761360	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10761363	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10821407	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10821411	0.85[EUR][1000 genomes]
rs10993386	0.85[EUR][1000 genomes]
rs12553916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1382411	0.95[AFR][1000 genomes]
rs1382412	0.95[AFR][1000 genomes]
rs1530331	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1542108	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16911856	0.87[AFR][1000 genomes]
rs17355875	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs191654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099868	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2165715	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs242260	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2584805	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356125	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356128	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356132	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356133	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356136	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs356139	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356145	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356147	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356148	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367319	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3910730	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs397783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs397806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41316526	0.95[AFR][1000 genomes]
rs422502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4332191	0.85[EUR][1000 genomes]
rs438742	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456276	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457795	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4612413	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743968	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4743970	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743972	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4743973	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4744382	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744387	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4744388	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744402	0.84[AFR][1000 genomes]
rs555799	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56198429	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs562605	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56317174	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58281499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60553517	0.82[AFR][1000 genomes]
rs61086657	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6479569	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479575	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479576	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479577	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6479578	0.85[EUR][1000 genomes]
rs6479579	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6479581	0.85[EUR][1000 genomes]
rs6479582	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6479583	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs66495734	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66642068	0.95[AFR][1000 genomes]
rs66710673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66863985	0.95[AFR][1000 genomes]
rs67208365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68090960	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68091393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7019602	0.85[EUR][1000 genomes]
rs7022963	0.85[EUR][1000 genomes]
rs7025100	0.85[EUR][1000 genomes]
rs7025934	0.87[EUR][1000 genomes]
rs7026714	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7035166	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7037239	0.82[AFR][1000 genomes]
rs7038519	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7038891	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7044371	0.85[EUR][1000 genomes]
rs7047478	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72747019	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7341710	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73532323	0.82[AFR][1000 genomes]
rs73532332	0.82[AFR][1000 genomes]
rs73532340	0.82[AFR][1000 genomes]
rs73532355	0.82[AFR][1000 genomes]
rs73534109	0.82[AFR][1000 genomes]
rs73534113	0.82[AFR][1000 genomes]
rs73534154	0.82[AFR][1000 genomes]
rs73534159	0.82[AFR][1000 genomes]
rs73536042	0.82[AFR][1000 genomes]
rs73536067	0.82[AFR][1000 genomes]
rs73536074	0.82[AFR][1000 genomes]
rs73538140	0.82[AFR][1000 genomes]
rs73538152	0.82[AFR][1000 genomes]
rs73538177	0.95[AFR][1000 genomes]
rs73540059	0.82[AFR][1000 genomes]
rs73540062	0.82[AFR][1000 genomes]
rs7855781	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867856	0.85[EUR][1000 genomes]
rs7870679	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs894426	0.85[EUR][1000 genomes]
rs894428	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9409589	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041922	chr9:97444976-97536753	Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97489600-97524800	Weak transcription	Esophagus	oesophagus
2	chr9:97489800-97521600	Weak transcription	Fetal Thymus	thymus
3	chr9:97489800-97522000	Weak transcription	Thymus	Thymus
4	chr9:97489800-97522400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:97490000-97519400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:97490000-97521600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:97490200-97519200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:97497000-97522000	Weak transcription	Placenta	Placenta
9	chr9:97497200-97522200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr9:97502800-97518800	Weak transcription	K562	blood
11	chr9:97503200-97522400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr9:97503800-97518800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:97504400-97522600	Weak transcription	Ovary	ovary
14	chr9:97504600-97521800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:97505200-97522200	Weak transcription	NHLF	lung
16	chr9:97506200-97521600	Weak transcription	Fetal Stomach	stomach
17	chr9:97506200-97533400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr9:97506400-97522000	Weak transcription	Lung	lung
19	chr9:97506400-97522200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:97506400-97526000	Weak transcription	Small Intestine	intestine
21	chr9:97509000-97522600	Weak transcription	Gastric	stomach
22	chr9:97509200-97536000	Weak transcription	Pancreas	Pancrea
23	chr9:97509400-97519000	Weak transcription	NH-A	brain
24	chr9:97509800-97519000	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:97510000-97512800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:97510800-97513600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:97511000-97512800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:97511000-97513000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
29	chr9:97511200-97522200	Weak transcription	Fetal Brain Male	brain
30	chr9:97511400-97512800	ZNF genes & repeats	Fetal Intestine Large	intestine
31	chr9:97511800-97519000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:97511800-97522000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:97512000-97519200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr9:97512000-97522400	Weak transcription	HepG2	liver
35	chr9:97512200-97513600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:97512400-97514200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:97512400-97519000	Weak transcription	Brain Substantia Nigra	brain
38	chr9:97512400-97519200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:97512400-97522400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:97512600-97513000	Weak transcription	Osteobl	bone
41	chr9:97512600-97513600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:97512600-97513800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr9:97512600-97514200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:97512600-97516600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:97512600-97518800	Weak transcription	HSMMtube	muscle
46	chr9:97512600-97519000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr9:97512600-97519000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:97512600-97519000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr9:97512600-97519000	Weak transcription	Left Ventricle	heart
50	chr9:97512600-97519000	Weak transcription	A549	lung

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