Variant report

Variant	rs17005829
Chromosome Location	chr3:69454849-69454850
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	chr3:69433963..69436912-chr3:69454119..69457021,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114541	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10510974	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11916346	0.88[AFR][1000 genomes]
rs11917290	0.88[AFR][1000 genomes]
rs11919150	0.88[AFR][1000 genomes]
rs11921571	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11926441	1.00[AMR][1000 genomes]
rs11928996	0.85[AFR][1000 genomes]
rs17005793	1.00[AMR][1000 genomes]
rs17005804	1.00[AMR][1000 genomes]
rs17005815	0.85[AFR][1000 genomes]
rs17005821	0.88[AFR][1000 genomes]
rs17005825	1.00[AMR][1000 genomes]
rs17005826	0.88[AFR][1000 genomes]
rs17005831	0.88[AFR][1000 genomes]
rs17005837	0.85[AFR][1000 genomes]
rs17005844	0.84[AFR][1000 genomes]
rs17005849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17043802	1.00[AMR][1000 genomes]
rs72937857	1.00[AMR][1000 genomes]
rs72937877	0.82[AFR][1000 genomes]
rs72937883	0.82[AFR][1000 genomes]
rs72937885	0.82[AFR][1000 genomes]
rs72937887	0.85[AFR][1000 genomes]
rs72937889	0.85[AFR][1000 genomes]
rs72937895	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72937901	0.87[AFR][1000 genomes]
rs72937902	0.88[AFR][1000 genomes]
rs72939655	0.96[AFR][1000 genomes]
rs72939706	0.88[AFR][1000 genomes]
rs72939709	0.88[AFR][1000 genomes]
rs72939711	0.88[AFR][1000 genomes]
rs72939718	0.88[AFR][1000 genomes]
rs72939723	0.88[AFR][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:21 , 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	chr3:69453800-69455000	ZNF genes & repeats	Brain Germinal Matrix	brain
3	chr3:69453800-69455000	ZNF genes & repeats	Fetal Brain Male	brain
4	chr3:69453800-69455000	ZNF genes & repeats	Fetal Lung	lung
5	chr3:69453800-69455600	ZNF genes & repeats	HMEC	breast
6	chr3:69453800-69456200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:69454000-69455000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:69454200-69455000	ZNF genes & repeats	NHEK	skin
9	chr3:69454400-69455000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
10	chr3:69454400-69455000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:69454600-69455400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:69454600-69456000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:69454800-69455200	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:69454800-69455200	Weak transcription	Brain Substantia Nigra	brain
15	chr3:69454800-69455400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:69454800-69455400	Enhancers	Brain Angular Gyrus	brain
17	chr3:69454800-69455400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:69454800-69455400	Weak transcription	Lung	lung
19	chr3:69454800-69456000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:69454800-69458600	Weak transcription	Fetal Brain Female	brain
21	chr3:69454800-69459000	Weak transcription	Monocytes-CD14+_RO01746	blood

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