Variant report

Variant	rs28364399
Chromosome Location	chr15:42678518-42678519
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42678390..42681163-chr15:42692112..42694875,2	K562	blood:

Variant related genes	Relation type
ENSG00000092529	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12441027	1.00[MEX][hapmap]
rs1678998	1.00[MEX][hapmap]
rs16972927	1.00[EUR][1000 genomes]
rs16972930	1.00[EUR][1000 genomes]
rs16972969	1.00[EUR][1000 genomes]
rs16973015	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16973018	1.00[EUR][1000 genomes]
rs16973022	1.00[EUR][1000 genomes]
rs16973177	0.83[EUR][1000 genomes]
rs16973182	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16973184	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16973188	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16973200	0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973206	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16973233	1.00[MEX][hapmap]
rs17593	0.87[ASW][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2412694	1.00[MEX][hapmap]
rs2412697	1.00[MEX][hapmap]
rs28364383	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28364385	0.80[AFR][1000 genomes]
rs28364387	1.00[EUR][1000 genomes]
rs28364395	1.00[MEX][hapmap]
rs28364396	1.00[MEX][hapmap]
rs28364407	1.00[MEX][hapmap]
rs28364423	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28364432	1.00[MEX][hapmap]
rs28364443	1.00[MEX][hapmap]
rs28364485	1.00[MEX][hapmap]
rs28364496	1.00[MEX][hapmap]
rs28364534	1.00[MEX][hapmap]
rs4307925	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4486855	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4516202	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4923941	1.00[MEX][hapmap]
rs4924650	1.00[MEX][hapmap]
rs4924668	1.00[MEX][hapmap]
rs4924669	1.00[MEX][hapmap]
rs4924671	1.00[MEX][hapmap]
rs7167683	0.87[ASW][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7174880	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7176832	1.00[MEX][hapmap]
rs728507	0.83[EUR][1000 genomes]
rs728508	0.83[EUR][1000 genomes]
rs728509	0.83[EUR][1000 genomes]
rs728510	1.00[EUR][1000 genomes]
rs8024452	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8026890	0.83[EUR][1000 genomes]
rs8027800	0.83[EUR][1000 genomes]
rs8033108	0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8033734	0.87[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8033882	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8033960	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8035332	0.83[EUR][1000 genomes]
rs8035521	0.83[EUR][1000 genomes]
rs8037627	1.00[MEX][hapmap]
rs8038771	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8038967	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8039470	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8040129	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8040726	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs934877	1.00[EUR][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	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	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42646000-42678600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:42652800-42684400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:42653200-42691600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:42656000-42678800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:42656800-42693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:42657200-42678800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:42663000-42691400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:42672400-42688800	Weak transcription	Esophagus	oesophagus
10	chr15:42673400-42691800	Weak transcription	Primary T cells from cord blood	blood
11	chr15:42674000-42694400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:42674600-42682600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:42674600-42684400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:42675200-42683600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:42675200-42684800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr15:42675200-42702800	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:42675600-42691600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:42675800-42678800	Weak transcription	Brain Angular Gyrus	brain
19	chr15:42676200-42682400	Strong transcription	Liver	Liver
20	chr15:42676400-42679000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr15:42676400-42679200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr15:42676400-42679600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:42676400-42680600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:42676600-42678600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr15:42676600-42679200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:42676600-42679800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr15:42676600-42680000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:42676600-42680200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:42676800-42679000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:42676800-42679200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:42676800-42679600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:42676800-42680200	Genic enhancers	Fetal Muscle Leg	muscle
33	chr15:42676800-42680400	Strong transcription	Primary B cells from cord blood	blood
34	chr15:42676800-42693200	Weak transcription	Fetal Stomach	stomach
35	chr15:42677000-42693400	Weak transcription	GM12878-XiMat	blood
36	chr15:42677200-42679200	Enhancers	Psoas Muscle	Psoas
37	chr15:42677200-42684000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:42677400-42680000	Genic enhancers	Adipose Nuclei	Adipose
39	chr15:42677400-42687800	Weak transcription	Brain Substantia Nigra	brain
40	chr15:42677600-42678600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:42677600-42678800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:42677600-42679600	Enhancers	Fetal Muscle Trunk	muscle
43	chr15:42677600-42689000	Weak transcription	Right Ventricle	heart
44	chr15:42677800-42679000	Genic enhancers	Spleen	Spleen
45	chr15:42677800-42679200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:42677800-42679400	Enhancers	Fetal Thymus	thymus
47	chr15:42677800-42679600	Enhancers	K562	blood
48	chr15:42677800-42680200	Enhancers	HSMMtube	muscle
49	chr15:42677800-42682600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:42678000-42678800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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