Variant report

Variant	rs2954789
Chromosome Location	chr17:15372383-15372384
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	chr17:15371816..15373680-chr17:15385031..15387890,2	MCF-7	breast:
2	chr17:15370733..15374395-chr17:15375320..15379081,3	K562	blood:

Variant related genes	Relation type
ENSG00000239704	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11078303	0.83[ASN][1000 genomes]
rs11078305	0.87[ASN][1000 genomes]
rs11654512	0.95[ASN][1000 genomes]
rs11867442	0.84[ASN][1000 genomes]
rs11867475	0.93[ASN][1000 genomes]
rs12601385	0.82[ASN][1000 genomes]
rs12945384	0.82[ASN][1000 genomes]
rs2323735	0.95[ASN][1000 genomes]
rs2875141	0.87[ASN][1000 genomes]
rs2875142	0.94[ASN][1000 genomes]
rs2906972	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2906978	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2906981	0.86[AMR][1000 genomes]
rs2954783	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2954785	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2954786	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2954788	0.95[ASN][1000 genomes]
rs4791623	0.94[ASN][1000 genomes]
rs4792612	0.94[ASN][1000 genomes]
rs7218048	0.94[ASN][1000 genomes]
rs7219022	0.95[ASN][1000 genomes]
rs7219900	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15340600-15399600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:15341400-15375800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr17:15356800-15378000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr17:15357800-15375800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr17:15359200-15404600	Weak transcription	Primary T cells from cord blood	blood
6	chr17:15359400-15386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr17:15359600-15383000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:15361200-15387800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr17:15361400-15385400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:15361600-15373200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:15361800-15382000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr17:15367400-15372800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:15367400-15394200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr17:15367800-15375800	Weak transcription	Small Intestine	intestine
15	chr17:15368000-15373800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr17:15368000-15382800	Weak transcription	Hela-S3	cervix
17	chr17:15368000-15393600	Weak transcription	Aorta	Aorta
18	chr17:15368200-15378800	Weak transcription	Psoas Muscle	Psoas
19	chr17:15368200-15379000	Weak transcription	A549	lung
20	chr17:15368200-15386800	Weak transcription	Ovary	ovary
21	chr17:15368400-15372800	Weak transcription	HUVEC	blood vessel
22	chr17:15368400-15405400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr17:15368600-15372800	Weak transcription	Brain Hippocampus Middle	brain
24	chr17:15368600-15379200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr17:15368600-15385600	Weak transcription	Fetal Brain Female	brain
26	chr17:15368800-15372400	Weak transcription	HSMM	muscle
27	chr17:15368800-15372600	Weak transcription	HepG2	liver
28	chr17:15368800-15376200	Weak transcription	Fetal Lung	lung
29	chr17:15368800-15382400	Weak transcription	Spleen	Spleen
30	chr17:15368800-15394000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:15369000-15372800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr17:15369000-15393600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:15369000-15401600	Weak transcription	Brain Germinal Matrix	brain
34	chr17:15369200-15372600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr17:15369200-15405000	Weak transcription	Esophagus	oesophagus
36	chr17:15369400-15382200	Weak transcription	Lung	lung
37	chr17:15369600-15386800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr17:15369800-15372600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr17:15370400-15372600	Enhancers	Fetal Intestine Small	intestine
40	chr17:15370600-15375200	Enhancers	Fetal Intestine Large	intestine
41	chr17:15370800-15373600	Enhancers	Fetal Muscle Leg	muscle
42	chr17:15371000-15372400	Enhancers	Fetal Heart	heart
43	chr17:15371000-15372800	Enhancers	Right Ventricle	heart
44	chr17:15371000-15373600	Enhancers	HSMMtube	muscle
45	chr17:15371000-15374400	Enhancers	Duodenum Mucosa	Duodenum
46	chr17:15371000-15375800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr17:15371200-15377000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr17:15371400-15373200	Enhancers	Fetal Muscle Trunk	muscle
49	chr17:15371400-15373400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr17:15371600-15374000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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