Variant report

Variant	rs17005844
Chromosome Location	chr3:69455414-69455415
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	chr3:69433963..69436912-chr3:69454119..69457021,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114541	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10510974	0.81[AFR][1000 genomes]
rs11916346	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11917290	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11919150	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11921571	0.83[AFR][1000 genomes]
rs11923981	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11928996	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17005815	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17005821	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17005826	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17005829	0.84[AFR][1000 genomes]
rs17005831	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17005837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17005849	0.84[AFR][1000 genomes]
rs72937861	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72937877	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72937880	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72937883	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72937885	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72937887	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72937889	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72937895	0.81[AFR][1000 genomes]
rs72937901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72937902	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72939655	0.81[AFR][1000 genomes]
rs72939706	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72939709	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72939711	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72939718	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72939723	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2760780	chr3:69413876-69513947	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3426797	chr3:69433086-69777229	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69450600-69461400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:69453800-69455600	ZNF genes & repeats	HMEC	breast
3	chr3:69453800-69456200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:69454600-69456000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:69454800-69456000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:69454800-69458600	Weak transcription	Fetal Brain Female	brain
7	chr3:69454800-69459000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:69455000-69458200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:69455000-69458800	Strong transcription	NHEK	skin
10	chr3:69455200-69455600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:69455200-69456000	Enhancers	Adipose Nuclei	Adipose
12	chr3:69455200-69456000	Enhancers	Brain Hippocampus Middle	brain
13	chr3:69455200-69456200	Enhancers	Fetal Lung	lung
14	chr3:69455200-69456400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:69455400-69455600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:69455400-69455600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:69455400-69455800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:69455400-69455800	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr3:69455400-69455800	Enhancers	Brain Anterior Caudate	brain
20	chr3:69455400-69455800	Enhancers	Brain Cingulate Gyrus	brain
21	chr3:69455400-69455800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:69455400-69455800	Flanking Active TSS	Brain Substantia Nigra	brain
23	chr3:69455400-69455800	Enhancers	Fetal Stomach	stomach
24	chr3:69455400-69455800	Enhancers	Left Ventricle	heart
25	chr3:69455400-69455800	Enhancers	Lung	lung
26	chr3:69455400-69455800	Enhancers	Right Atrium	heart
27	chr3:69455400-69455800	Enhancers	HSMMtube	muscle
28	chr3:69455400-69456000	Enhancers	Fetal Brain Male	brain
29	chr3:69455400-69456200	Enhancers	Brain Germinal Matrix	brain
30	chr3:69455400-69456200	Enhancers	Fetal Muscle Leg	muscle

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