Variant report

Variant	rs9332039
Chromosome Location	chr13:49078523-49078524
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	chr13:49075530..49077233-chr13:49077933..49080570,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs4151570	1.00[AMR][1000 genomes]
rs4151577	1.00[AMR][1000 genomes]
rs4151619	0.90[AFR][1000 genomes]
rs4151630	0.90[AFR][1000 genomes]
rs6561447	1.00[AMR][1000 genomes]
rs6561450	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6561451	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6561453	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6561454	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7317090	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7321483	1.00[AFR][1000 genomes]
rs7322265	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7322855	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7325162	0.82[AFR][1000 genomes]
rs7332828	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7334590	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7984753	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7987986	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7988909	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7989808	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9331963	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9331967	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9331992	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332004	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332006	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332010	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332020	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332023	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332024	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332027	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332047	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9332074	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9332077	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9332081	1.00[YRI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:49063000-49087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:49066800-49080200	Weak transcription	Colonic Mucosa	Colon
4	chr13:49067000-49080200	Weak transcription	Psoas Muscle	Psoas
5	chr13:49067000-49084200	Weak transcription	Ovary	ovary
6	chr13:49067200-49079200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr13:49067200-49079600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr13:49067200-49080200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr13:49067200-49105200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr13:49067200-49105400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr13:49067800-49078600	Weak transcription	Placenta	Placenta
12	chr13:49067800-49078600	Weak transcription	Right Atrium	heart
13	chr13:49067800-49078600	Weak transcription	Stomach Mucosa	stomach
14	chr13:49067800-49079400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr13:49067800-49098000	Weak transcription	Right Ventricle	heart
16	chr13:49068000-49105600	Weak transcription	Gastric	stomach
17	chr13:49068200-49102600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr13:49068400-49081000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr13:49070400-49078600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr13:49071200-49105600	Weak transcription	Fetal Brain Male	brain
21	chr13:49071600-49078600	Weak transcription	Thymus	Thymus
22	chr13:49071600-49078800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:49071800-49079200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr13:49071800-49086200	Strong transcription	Fetal Stomach	stomach
25	chr13:49071800-49105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr13:49072000-49088400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr13:49072200-49079400	Weak transcription	Brain Angular Gyrus	brain
28	chr13:49072200-49080200	Weak transcription	Spleen	Spleen
29	chr13:49072200-49085800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr13:49072200-49095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr13:49072400-49078800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr13:49072400-49079800	Weak transcription	Brain Substantia Nigra	brain
33	chr13:49072400-49080200	Weak transcription	Aorta	Aorta
34	chr13:49072400-49080400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr13:49073000-49078800	Strong transcription	Fetal Muscle Leg	muscle
36	chr13:49073200-49085800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr13:49073400-49080200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr13:49073600-49087800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr13:49073800-49081200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr13:49074200-49078800	Weak transcription	Brain Hippocampus Middle	brain
41	chr13:49074200-49079400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr13:49074200-49079600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:49074800-49083000	Weak transcription	Fetal Intestine Small	intestine
44	chr13:49075000-49078800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr13:49075200-49078600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr13:49075400-49080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr13:49075400-49085800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr13:49075600-49078600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:49075600-49078600	Weak transcription	HSMMtube	muscle
50	chr13:49075600-49078800	Weak transcription	Adipose Nuclei	Adipose

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