Variant report

Variant	rs9830920
Chromosome Location	chr3:50639470-50639471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50624498..50626370-chr3:50639043..50642026,2	K562	blood:
2	chr3:50373496..50376492-chr3:50637687..50640592,4	K562	blood:
3	chr3:50626963..50632967-chr3:50633102..50640850,17	K562	blood:
4	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
5	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:
6	chr3:50596509..50599002-chr3:50637858..50640256,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114735	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000088543	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1034405	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11130252	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs129310	0.81[EUR][1000 genomes]
rs13076850	0.90[EUR][1000 genomes]
rs13083004	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13084476	0.86[EUR][1000 genomes]
rs13091933	0.87[EUR][1000 genomes]
rs13094336	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13094785	0.81[AMR][1000 genomes]
rs17787569	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs201194	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs201196	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs201197	0.89[EUR][1000 genomes]
rs201198	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2227280	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2232248	0.83[EUR][1000 genomes]
rs2232253	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2269507	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2355321	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2355323	0.82[EUR][1000 genomes]
rs34202063	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34267788	0.82[EUR][1000 genomes]
rs34399912	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34434811	0.82[EUR][1000 genomes]
rs34584636	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34756253	0.86[EUR][1000 genomes]
rs34889917	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35655236	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35690191	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35714264	0.87[EUR][1000 genomes]
rs35864641	0.82[EUR][1000 genomes]
rs3804627	0.82[EUR][1000 genomes]
rs399484	0.88[EUR][1000 genomes]
rs399971	0.80[EUR][1000 genomes]
rs417592	0.82[EUR][1000 genomes]
rs441516	0.82[EUR][1000 genomes]
rs443030	0.81[EUR][1000 genomes]
rs4533647	0.82[EUR][1000 genomes]
rs453570	0.82[EUR][1000 genomes]
rs490634	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59949730	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs622502	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67588094	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6768300	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs67813889	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6784166	0.87[EUR][1000 genomes]
rs6787521	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs695170	0.82[EUR][1000 genomes]
rs71326937	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73082948	0.80[EUR][1000 genomes]
rs7646236	0.82[EUR][1000 genomes]
rs809451	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50635800-50640400	Enhancers	Placenta	Placenta
2	chr3:50636000-50641200	Enhancers	Lung	lung
3	chr3:50636000-50641400	Enhancers	Fetal Thymus	thymus
4	chr3:50636000-50641600	Enhancers	Esophagus	oesophagus
5	chr3:50636200-50640600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:50636400-50640600	Enhancers	Right Atrium	heart
7	chr3:50636400-50641000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:50636400-50641600	Enhancers	Pancreas	Pancrea
9	chr3:50636600-50639600	Enhancers	Spleen	Spleen
10	chr3:50636600-50640400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:50636600-50640600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:50636600-50643600	Enhancers	Left Ventricle	heart
13	chr3:50636800-50640600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:50636800-50641600	Enhancers	Gastric	stomach
15	chr3:50636800-50646000	Genic enhancers	Fetal Intestine Small	intestine
16	chr3:50637000-50639800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr3:50637000-50640400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:50637000-50640400	Enhancers	Brain Angular Gyrus	brain
19	chr3:50637000-50640800	Enhancers	Primary hematopoietic stem cells	blood
20	chr3:50637200-50640200	Enhancers	Primary B cells from peripheral blood	blood
21	chr3:50637200-50640400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:50637400-50639800	Flanking Active TSS	K562	blood
23	chr3:50637400-50640000	Enhancers	Brain Substantia Nigra	brain
24	chr3:50637400-50640200	Enhancers	Psoas Muscle	Psoas
25	chr3:50637400-50640600	Flanking Active TSS	Dnd41	blood
26	chr3:50637600-50640000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:50637600-50640000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr3:50637600-50640400	Enhancers	Primary B cells from cord blood	blood
29	chr3:50637600-50641200	Enhancers	Small Intestine	intestine
30	chr3:50637800-50639800	Flanking Active TSS	Colonic Mucosa	Colon
31	chr3:50637800-50640200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:50637800-50640400	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr3:50638000-50639600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr3:50638000-50639600	Enhancers	Fetal Brain Male	brain
35	chr3:50638000-50640000	Enhancers	Thymus	Thymus
36	chr3:50638000-50640000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr3:50638000-50640200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr3:50638000-50640400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:50638000-50641200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:50638200-50639800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:50638200-50639800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr3:50638200-50640000	Enhancers	NH-A	brain
43	chr3:50638200-50640200	Enhancers	Placenta Amnion	Placenta Amnion
44	chr3:50638200-50640200	Flanking Active TSS	HepG2	liver
45	chr3:50638200-50640600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr3:50638400-50639800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:50638400-50639800	Weak transcription	Ovary	ovary
48	chr3:50638400-50639800	Enhancers	HUVEC	blood vessel
49	chr3:50638400-50640000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:50638400-50640600	Enhancers	Sigmoid Colon	Sigmoid Colon

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