Variant report

Variant	rs28628290
Chromosome Location	chr15:76027402-76027403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr15:76027141-76027676	GM12878	blood:	n/a	n/a
2	SPI1	chr15:76027380-76027669	GM12891	blood:	n/a	n/a
3	SPI1	chr15:76027319-76027667	GM12878	blood:	n/a	n/a
4	POU2F2	chr15:76027206-76027793	GM12878	blood:	n/a	n/a
5	PAX5	chr15:76027135-76027543	GM12878	blood:	n/a	n/a
6	PAX5	chr15:76027124-76027812	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:76027340-76027558	GM12878	blood:	n/a	n/a
8	SPI1	chr15:76027383-76027542	GM12878	blood:	n/a	n/a
9	SPI1	chr15:76027398-76027567	K562	blood:	n/a	n/a
10	PAX5	chr15:76027243-76027604	GM12878	blood:	n/a	n/a
11	IRF4	chr15:76027315-76027610	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76021736..76024634-chr15:76026770..76028436,2	MCF-7	breast:
2	chr15:76026055..76028108-chr15:76032882..76034389,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CSPG4-1	chr15:76027179-76028083	NONHSAT047365

No data

Variant related genes	Relation type
ENSG00000260288	TF binding region
ENSG00000256530	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12102136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16967294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16967508	1.00[EUR][1000 genomes]
rs28372561	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28395383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28396803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28398053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28412110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28413637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28414758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28420558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28432282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28447345	1.00[EUR][1000 genomes]
rs28450740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28461701	1.00[EUR][1000 genomes]
rs28504376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28505697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28510991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28519586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28521156	1.00[EUR][1000 genomes]
rs28530778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28533248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28550881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28567605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28628820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28645531	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28664638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28677951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28695912	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28711283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28727341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3991368	1.00[AMR][1000 genomes]
rs56686272	1.00[AMR][1000 genomes]
rs57267837	1.00[AMR][1000 genomes]
rs58167659	1.00[AMR][1000 genomes]
rs58689645	1.00[AMR][1000 genomes]
rs58840197	1.00[EUR][1000 genomes]
rs59944002	1.00[AMR][1000 genomes]
rs60159975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60465775	1.00[AMR][1000 genomes]
rs60544586	1.00[AMR][1000 genomes]
rs73439281	1.00[AMR][1000 genomes]
rs73439290	1.00[AMR][1000 genomes]
rs73439302	1.00[AMR][1000 genomes]
rs73442996	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73444997	1.00[AMR][1000 genomes]
rs74026527	1.00[EUR][1000 genomes]
rs8026666	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8033538	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8041384	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
4	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76013800-76029800	Weak transcription	HSMM	muscle
2	chr15:76020600-76030200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:76021000-76030200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:76021000-76030200	Weak transcription	HMEC	breast
5	chr15:76021400-76029600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:76022000-76028800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:76024200-76027800	Enhancers	Spleen	Spleen
8	chr15:76024200-76029400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:76024200-76029400	Weak transcription	Fetal Brain Female	brain
10	chr15:76024400-76030400	Weak transcription	Primary B cells from cord blood	blood
11	chr15:76024600-76030200	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:76024800-76029600	Weak transcription	Brain Germinal Matrix	brain
13	chr15:76024800-76030400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:76025000-76030200	Weak transcription	NHDF-Ad	bronchial
15	chr15:76025000-76030400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:76025200-76027800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:76025200-76028200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:76025200-76028800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:76025200-76029200	Weak transcription	Brain Angular Gyrus	brain
20	chr15:76025200-76030200	Weak transcription	Colonic Mucosa	Colon
21	chr15:76025200-76030200	Weak transcription	Fetal Heart	heart
22	chr15:76025200-76030200	Weak transcription	Fetal Intestine Large	intestine
23	chr15:76025200-76030400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:76025200-76030400	Weak transcription	Right Atrium	heart
25	chr15:76025400-76028600	Weak transcription	Esophagus	oesophagus
26	chr15:76025400-76028800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:76025400-76029400	Weak transcription	Adipose Nuclei	Adipose
28	chr15:76025400-76029600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:76025400-76030200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:76025400-76030200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr15:76025400-76030200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:76025400-76030200	Weak transcription	K562	blood
33	chr15:76025400-76030400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:76025600-76027600	Weak transcription	Fetal Thymus	thymus
35	chr15:76025600-76028600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:76025600-76028800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr15:76025600-76028800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:76025600-76028800	Weak transcription	Stomach Mucosa	stomach
39	chr15:76025600-76029400	Weak transcription	Fetal Brain Male	brain
40	chr15:76025600-76029600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:76025600-76029600	Weak transcription	Liver	Liver
42	chr15:76025600-76029800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:76025600-76030200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr15:76025600-76030200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:76025600-76030200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr15:76025600-76030200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:76025600-76030200	Weak transcription	Fetal Lung	lung
48	chr15:76025600-76030200	Weak transcription	Ovary	ovary
49	chr15:76025600-76030200	Weak transcription	Pancreas	Pancrea
50	chr15:76025600-76030200	Weak transcription	Rectal Mucosa Donor 31	rectum

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