Variant report

Variant	rs28744517
Chromosome Location	chr14:104038418-104038419
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104026574..104032100-chr14:104033737..104038565,9	MCF-7	breast:
2	chr14:104038173..104039044-chr14:104145432..104146025,3	MCF-7	breast:
3	chr14:104037950..104041311-chr14:104041482..104045327,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264904	Chromatin interaction
ENSG00000256053	Chromatin interaction
ENSG00000166170	Chromatin interaction
ENSG00000126214	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10134399	0.82[EUR][1000 genomes]
rs10140410	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10143293	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10149249	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11621777	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11626658	0.91[EUR][1000 genomes]
rs2274268	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2274269	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28513222	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28514618	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28660416	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55864158	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56017123	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57447494	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59281218	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60802358	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61996716	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61996717	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61996718	0.84[ASN][1000 genomes]
rs61996721	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7142883	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7154587	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7154948	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7693	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs942863	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902297	chr14:103956182-104061646	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902298	chr14:103959289-104061646	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv902299	chr14:103967504-104061646	Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv902304	chr14:103979953-104061646	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv902305	chr14:103979953-104073551	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers 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	43 gene(s)	inside rSNPs	diseases
9	nsv566022	chr14:104007555-104092789	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28744517	APOPT1	cis	Muscle Skeletal	GTEx
rs28744517	BAG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104030000-104045000	Weak transcription	Aorta	Aorta
2	chr14:104030200-104040600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:104030200-104044800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:104030400-104040600	Weak transcription	Lung	lung
5	chr14:104030600-104039200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr14:104030600-104039600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr14:104030600-104040600	Weak transcription	HSMMtube	muscle
8	chr14:104030600-104040800	Weak transcription	Right Ventricle	heart
9	chr14:104030600-104042400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr14:104030600-104042800	Weak transcription	Fetal Heart	heart
11	chr14:104030800-104038600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr14:104030800-104038600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr14:104030800-104038600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr14:104030800-104038600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr14:104030800-104038600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr14:104030800-104038800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr14:104030800-104038800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr14:104030800-104038800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr14:104030800-104038800	Weak transcription	Fetal Intestine Large	intestine
20	chr14:104030800-104039000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr14:104030800-104039400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr14:104030800-104039400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr14:104030800-104039600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr14:104030800-104039800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr14:104030800-104040000	Weak transcription	NH-A	brain
26	chr14:104030800-104040200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr14:104030800-104040200	Weak transcription	HSMM	muscle
28	chr14:104030800-104040400	Weak transcription	Colonic Mucosa	Colon
29	chr14:104030800-104040400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr14:104030800-104040600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr14:104030800-104040600	Weak transcription	Brain Angular Gyrus	brain
32	chr14:104030800-104040600	Weak transcription	Colon Smooth Muscle	Colon
33	chr14:104030800-104040600	Weak transcription	Fetal Thymus	thymus
34	chr14:104030800-104040600	Weak transcription	Psoas Muscle	Psoas
35	chr14:104030800-104040600	Weak transcription	Spleen	Spleen
36	chr14:104030800-104040600	Weak transcription	K562	blood
37	chr14:104030800-104040600	Weak transcription	NHLF	lung
38	chr14:104030800-104042600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr14:104030800-104044000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr14:104030800-104073200	Weak transcription	Small Intestine	intestine
41	chr14:104031000-104038600	Weak transcription	Primary B cells from cord blood	blood
42	chr14:104031000-104038600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr14:104031000-104038800	Weak transcription	HepG2	liver
44	chr14:104031000-104039000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr14:104031000-104040000	Weak transcription	Thymus	Thymus
46	chr14:104031000-104040200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr14:104031000-104040200	Weak transcription	NHEK	skin
48	chr14:104031000-104040600	Weak transcription	HMEC	breast
49	chr14:104031400-104039400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr14:104031400-104039800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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