Variant report

Variant	rs8028745
Chromosome Location	chr15:50600116-50600117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr15:50599902-50600380	K562	blood:	n/a	n/a
2	CBX3	chr15:50599952-50600247	K562	blood:	n/a	n/a
3	KAP1	chr15:50599963-50600514	K562	blood:	n/a	n/a
4	MEF2A	chr15:50599969-50600406	K562	blood:	n/a	chr15:50600170-50600185

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50474513..50476757-chr15:50599971..50603142,3	MCF-7	breast:

Variant related genes	Relation type
GABPB1	TF binding region
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10083714	0.82[ASN][1000 genomes]
rs10152574	0.92[ASN][1000 genomes]
rs11491094	0.82[ASN][1000 genomes]
rs16963562	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs16963571	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963573	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963578	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963582	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1896169	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1955101	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55697237	0.92[ASN][1000 genomes]
rs55774471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55950921	0.92[ASN][1000 genomes]
rs56812974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58903525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59847008	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60893904	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs717025	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7177488	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012326	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012366	0.92[ASN][1000 genomes]
rs74012367	0.92[ASN][1000 genomes]
rs8029259	0.82[ASN][1000 genomes]
rs8029439	0.82[ASN][1000 genomes]
rs8034492	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8040420	0.86[ASN][1000 genomes]
rs8040483	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs953159	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9652452	0.82[ASN][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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50570400-50606600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:50570800-50600600	Weak transcription	Spleen	Spleen
3	chr15:50574400-50602000	Weak transcription	Small Intestine	intestine
4	chr15:50575200-50601000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:50578200-50600400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:50580400-50605000	Weak transcription	Fetal Heart	heart
7	chr15:50580800-50600600	Weak transcription	Pancreas	Pancrea
8	chr15:50580800-50638400	Weak transcription	NHEK	skin
9	chr15:50581000-50600600	Weak transcription	Colonic Mucosa	Colon
10	chr15:50587200-50600400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:50589800-50602600	Weak transcription	Gastric	stomach
12	chr15:50592400-50600200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:50592400-50600600	Weak transcription	Esophagus	oesophagus
14	chr15:50592600-50600400	Weak transcription	NHLF	lung
15	chr15:50593400-50600600	Weak transcription	Psoas Muscle	Psoas
16	chr15:50593400-50602400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:50593600-50600200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:50593600-50600200	Weak transcription	Brain Angular Gyrus	brain
19	chr15:50593600-50600200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:50593600-50600200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr15:50593600-50600600	Weak transcription	Left Ventricle	heart
22	chr15:50593600-50600600	Weak transcription	Lung	lung
23	chr15:50593600-50602400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:50593600-50605200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:50593800-50600400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:50594000-50600200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:50594000-50600200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:50594000-50608400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:50594000-50610200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:50594200-50600200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:50594200-50600600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:50594200-50603600	Weak transcription	NH-A	brain
33	chr15:50594200-50608400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:50594400-50600200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:50594600-50610400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:50594800-50600600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:50594800-50604400	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:50595000-50600400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:50595600-50600200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr15:50595600-50600400	Weak transcription	Ovary	ovary
41	chr15:50596400-50600200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:50596400-50600200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr15:50596400-50600200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:50596400-50600200	Weak transcription	Hela-S3	cervix
45	chr15:50596400-50600200	Weak transcription	HepG2	liver
46	chr15:50596400-50600600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr15:50596400-50601000	Weak transcription	HMEC	breast
48	chr15:50596400-50623400	Weak transcription	Aorta	Aorta
49	chr15:50596600-50600600	Weak transcription	Fetal Thymus	thymus
50	chr15:50596600-50608000	Weak transcription	Liver	Liver

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