Variant report

Variant	rs6890684
Chromosome Location	chr5:60615886-60615887
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	chr5:60611558..60614120-chr5:60615826..60618466,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13169711	0.85[AMR][1000 genomes]
rs13170135	0.85[AMR][1000 genomes]
rs4132385	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4391122	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4546329	0.86[AMR][1000 genomes]
rs4583848	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4604142	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6449528	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6449529	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7701440	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7724551	0.84[AFR][1000 genomes];0.86[AMR][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	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60610000-60618600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:60610800-60618600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:60611200-60618200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:60611400-60618200	Weak transcription	NH-A	brain
5	chr5:60611400-60618800	Weak transcription	A549	lung
6	chr5:60611800-60618400	Weak transcription	HSMM	muscle
7	chr5:60613000-60618600	Weak transcription	Aorta	Aorta
8	chr5:60613400-60616400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:60613400-60616400	Enhancers	Brain Substantia Nigra	brain
10	chr5:60613400-60621000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr5:60614200-60617000	Enhancers	Primary B cells from peripheral blood	blood
12	chr5:60614200-60617400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr5:60614200-60617600	Enhancers	Fetal Lung	lung
14	chr5:60614400-60616200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr5:60614400-60616200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:60614400-60616200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:60614400-60616200	Enhancers	Fetal Brain Male	brain
18	chr5:60614600-60616000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr5:60614600-60616400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:60614600-60618600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:60614600-60618800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:60614600-60620000	Enhancers	Fetal Intestine Small	intestine
23	chr5:60614800-60616000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:60614800-60616000	Enhancers	Fetal Intestine Large	intestine
25	chr5:60614800-60616000	Enhancers	Fetal Stomach	stomach
26	chr5:60614800-60616600	Enhancers	Brain Cingulate Gyrus	brain
27	chr5:60614800-60617200	Enhancers	Colonic Mucosa	Colon
28	chr5:60614800-60617400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr5:60614800-60618200	Weak transcription	Osteobl	bone
30	chr5:60615000-60616000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr5:60615000-60616000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr5:60615000-60616200	Enhancers	Stomach Mucosa	stomach
33	chr5:60615000-60616400	Enhancers	Fetal Muscle Leg	muscle
34	chr5:60615000-60616600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:60615000-60616600	Enhancers	Fetal Thymus	thymus
36	chr5:60615000-60616800	Enhancers	Fetal Heart	heart
37	chr5:60615200-60616000	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr5:60615200-60616000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr5:60615200-60616000	Enhancers	Brain Germinal Matrix	brain
40	chr5:60615200-60616400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr5:60615400-60616000	Enhancers	Placenta	Placenta
42	chr5:60615400-60616400	Enhancers	Gastric	stomach
43	chr5:60615400-60616600	Enhancers	Left Ventricle	heart
44	chr5:60615400-60616600	Enhancers	Lung	lung
45	chr5:60615400-60616600	Enhancers	Spleen	Spleen
46	chr5:60615400-60617000	Enhancers	Esophagus	oesophagus
47	chr5:60615600-60616000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:60615600-60616000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:60615600-60616000	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr5:60615600-60616000	Enhancers	GM12878-XiMat	blood

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