Variant report

Variant	rs28364454
Chromosome Location	chr15:42686350-42686351
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42686331..42689560-chr15:42693488..42696057,3	K562	blood:
2	chr15:42660141..42662692-chr15:42684785..42686595,2	K562	blood:
3	chr15:42679521..42681202-chr15:42684595..42687043,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092529	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17592	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364389	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364392	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364395	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364396	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364407	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364432	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28364443	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364485	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364496	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364534	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7169432	1.00[AMR][1000 genomes]
rs7176832	1.00[ASW][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7182306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8028539	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv932995	chr15:42640015-42704121	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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	29 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	chr15:42653200-42691600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:42656800-42693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:42663000-42691400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:42672400-42688800	Weak transcription	Esophagus	oesophagus
6	chr15:42673400-42691800	Weak transcription	Primary T cells from cord blood	blood
7	chr15:42674000-42694400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:42675200-42702800	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:42675600-42691600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:42676800-42693200	Weak transcription	Fetal Stomach	stomach
11	chr15:42677000-42693400	Weak transcription	GM12878-XiMat	blood
12	chr15:42677400-42687800	Weak transcription	Brain Substantia Nigra	brain
13	chr15:42677600-42689000	Weak transcription	Right Ventricle	heart
14	chr15:42678200-42688000	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:42678400-42687400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:42678600-42691200	Weak transcription	Gastric	stomach
17	chr15:42678600-42706800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:42678800-42691600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:42678800-42694000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:42678800-42702800	Weak transcription	NHLF	lung
21	chr15:42679000-42687400	Weak transcription	Spleen	Spleen
22	chr15:42679000-42691400	Weak transcription	Thymus	Thymus
23	chr15:42679000-42706800	Weak transcription	Right Atrium	heart
24	chr15:42679200-42691600	Weak transcription	Brain Anterior Caudate	brain
25	chr15:42679200-42694000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:42679600-42691400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:42680000-42693200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:42680200-42690200	Strong transcription	Fetal Muscle Leg	muscle
29	chr15:42680200-42691400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:42680200-42694000	Weak transcription	Left Ventricle	heart
31	chr15:42680200-42696400	Weak transcription	HSMMtube	muscle
32	chr15:42680600-42691200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:42680600-42693600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr15:42681600-42695400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:42681800-42689000	Weak transcription	Psoas Muscle	Psoas
36	chr15:42681800-42694600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:42682000-42691600	Weak transcription	Adipose Nuclei	Adipose
38	chr15:42682000-42691800	Weak transcription	Ovary	ovary
39	chr15:42682200-42686800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr15:42682400-42688800	Weak transcription	Liver	Liver
41	chr15:42682400-42691600	Weak transcription	Aorta	Aorta
42	chr15:42682600-42691400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:42683800-42704600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr15:42684000-42691400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:42684600-42686400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:42684800-42686400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:42684800-42686400	Enhancers	Fetal Intestine Large	intestine
48	chr15:42684800-42686400	Enhancers	Fetal Intestine Small	intestine
49	chr15:42684800-42688800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr15:42685000-42686400	Weak transcription	Lung	lung

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