Variant report

Variant	rs28615486
Chromosome Location	chr15:100012805-100012806
allele	A/G
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	FOXA1	chr15:100012627-100012959	HepG2	liver:	n/a	n/a
2	FOXA1	chr15:100012598-100012996	HepG2	liver:	n/a	n/a
3	SMC3	chr15:100012710-100012910	HepG2	liver:	n/a	n/a
4	ARID3A	chr15:100012553-100012949	HepG2	liver:	n/a	n/a
5	FOXA1	chr15:100012625-100013027	HepG2	liver:	n/a	n/a
6	FOXA2	chr15:100012682-100012932	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:100010923..100013098-chr15:100015221..100016776,2	MCF-7	breast:
2	chr15:100005826..100008699-chr15:100011873..100013969,2	MCF-7	breast:

Variant related genes	Relation type
MEF2A	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12592753	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594174	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12595336	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901856	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902817	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12907047	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907380	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911709	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12915746	0.96[EUR][1000 genomes]
rs1992485	0.96[EUR][1000 genomes]
rs28538977	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2862089	0.86[EUR][1000 genomes]
rs34833026	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4965244	0.89[ASN][1000 genomes]
rs4965248	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4965249	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4965510	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4965511	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4965512	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58271980	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6598253	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66994542	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71399871	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7165608	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7165832	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7182803	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182877	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7182883	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8024609	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8027441	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv1050527	chr15:99983054-100035436	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv457278	chr15:100002468-100015179	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv570729	chr15:100002468-100015179	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100007800-100013000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr15:100008000-100013000	Weak transcription	Thymus	Thymus
3	chr15:100008000-100014400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:100008200-100013000	Weak transcription	Right Ventricle	heart
5	chr15:100008200-100020600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:100008400-100013600	Weak transcription	Lung	lung
7	chr15:100008400-100016600	Weak transcription	Hela-S3	cervix
8	chr15:100008800-100014400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:100011400-100013000	Weak transcription	GM12878-XiMat	blood
10	chr15:100012200-100015800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr15:100012400-100013000	Enhancers	Pancreas	Pancrea
12	chr15:100012400-100013000	Bivalent Enhancer	HepG2	liver
13	chr15:100012400-100013600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr15:100012400-100014400	Enhancers	Left Ventricle	heart
15	chr15:100012400-100018200	Enhancers	Stomach Mucosa	stomach
16	chr15:100012400-100018600	Enhancers	Spleen	Spleen
17	chr15:100012400-100018800	Enhancers	Right Atrium	heart
18	chr15:100012600-100015600	Enhancers	Ovary	ovary
19	chr15:100012600-100016000	Weak transcription	Small Intestine	intestine
20	chr15:100012600-100018600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr15:100012600-100019000	Enhancers	Fetal Heart	heart
22	chr15:100012800-100013000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:100012800-100013200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr15:100012800-100013800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr15:100012800-100013800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr15:100012800-100014000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:100012800-100015400	Weak transcription	NHEK	skin
28	chr15:100012800-100015600	Enhancers	Primary B cells from peripheral blood	blood
29	chr15:100012800-100016200	Weak transcription	NH-A	brain
30	chr15:100012800-100018800	Enhancers	Fetal Lung	lung

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