Variant report

Variant	rs28501391
Chromosome Location	chr15:79281163-79281164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:169)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:169 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr15:79280905-79281210	SK-N-SH_RA	brain:	n/a	n/a
2	STAT3	chr15:79280980-79281277	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr15:79280861-79281388	SK-N-SH	brain:	n/a	n/a
4	EP300	chr15:79280620-79281333	HepG2	liver:	n/a	n/a
5	JUND	chr15:79280859-79281318	A549	lung:	n/a	n/a
6	RUNX3	chr15:79280766-79281309	GM12878	blood:	n/a	n/a
7	MAFK	chr15:79281070-79281170	Hela-S3	cervix:	n/a	n/a
8	FOXA1	chr15:79280888-79281252	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:79280149-79281427	HepG2	liver:	n/a	n/a
10	USF1	chr15:79280885-79281201	HepG2	liver:	n/a	n/a
11	REST	chr15:79280845-79281269	HepG2	liver:	n/a	chr15:79280972-79280992
12	E2F6	chr15:79280596-79281362	A549	lung:	n/a	n/a
13	NFIC	chr15:79280850-79281320	GM12878	blood:	n/a	n/a
14	MAZ	chr15:79280845-79281332	HepG2	liver:	n/a	n/a
15	JUND	chr15:79280820-79281291	HepG2	liver:	n/a	n/a
16	JUN	chr15:79280981-79281181	K562	blood:	n/a	n/a
17	HNF4A	chr15:79280793-79281399	HepG2	liver:	n/a	n/a
18	USF1	chr15:79280880-79281176	SK-N-SH_RA	brain:	n/a	n/a
19	MYC	chr15:79280667-79281427	NB4	blood:	n/a	n/a
20	MAZ	chr15:79281047-79281180	Hela-S3	cervix:	n/a	n/a
21	USF1	chr15:79280896-79281230	A549	lung:	n/a	n/a
22	JUND	chr15:79280684-79281447	SK-N-SH	brain:	n/a	n/a
23	MAX	chr15:79280767-79281310	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr15:79280879-79281184	SK-N-SH	brain:	n/a	n/a
25	FOS	chr15:79280599-79281234	MCF10A-Er-Src	breast:	n/a	n/a
26	SP1	chr15:79280858-79281386	HepG2	liver:	n/a	n/a
27	MAX	chr15:79280904-79281239	Hela-S3	cervix:	n/a	n/a
28	MAFK	chr15:79280803-79281428	HepG2	liver:	n/a	n/a
29	HDAC2	chr15:79280734-79281338	HepG2	liver:	n/a	chr15:79281188-79281202 chr15:79280899-79280913 chr15:79281186-79281200 chr15:79281189-79281203 chr15:79281187-79281201 chr15:79281190-79281204
30	SIN3AK20	chr15:79280954-79281211	HepG2	liver:	n/a	n/a
31	TBP	chr15:79280499-79281314	GM12878	blood:	n/a	n/a
32	STAT3	chr15:79281022-79281496	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr15:79280829-79281239	MCF10A-Er-Src	breast:	n/a	n/a
34	FOSL2	chr15:79280755-79281319	HepG2	liver:	n/a	n/a
35	POLR2A	chr15:79280671-79281292	HepG2	liver:	n/a	n/a
36	MAX	chr15:79280581-79281439	A549	lung:	n/a	n/a
37	EP300	chr15:79280728-79281315	HepG2	liver:	n/a	n/a
38	CHD2	chr15:79280591-79281235	GM12878	blood:	n/a	n/a
39	USF1	chr15:79280875-79281230	HepG2	liver:	n/a	n/a
40	CEBPD	chr15:79280799-79281305	HepG2	liver:	n/a	n/a
41	POLR2A	chr15:79280697-79281342	U87	brain:	n/a	n/a
42	SMC3	chr15:79280849-79281391	HepG2	liver:	n/a	n/a
43	TBL1XR1	chr15:79280886-79281242	GM12878	blood:	n/a	n/a
44	MYC	chr15:79280668-79281338	HepG2	liver:	n/a	n/a
45	USF2	chr15:79280882-79281270	HepG2	liver:	n/a	n/a
46	USF1	chr15:79280903-79281246	A549	lung:	n/a	n/a
47	USF2	chr15:79280897-79281274	Hela-S3	cervix:	n/a	n/a
48	FOS	chr15:79280864-79281265	MCF10A-Er-Src	breast:	n/a	n/a
49	CUX1	chr15:79280671-79281246	GM12878	blood:	n/a	n/a
50	CEBPB	chr15:79281030-79281341	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:79223166..79226414-chr15:79279938..79282218,3	MCF-7	breast:
2	chr15:79267805..79270419-chr15:79279866..79282392,3	MCF-7	breast:
3	chr15:79270685..79272410-chr15:79279786..79282271,2	MCF-7	breast:

No data

Variant related genes	Relation type
RASGRF1	TF binding region
ENSG00000103811	Chromatin interaction
ENSG00000058335	Chromatin interaction
ENSG00000177699	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12101364	1.00[EUR][1000 genomes]
rs16970387	0.81[EUR][1000 genomes]
rs28368520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28391216	1.00[EUR][1000 genomes]
rs28407629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28427472	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28461937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28513164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28516885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28546944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28547879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28549817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28557276	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28565526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28567804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28587174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28603308	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28624404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28674868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28683537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28709904	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28716558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28718997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28722773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28738778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920807	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904433	chr15:79243571-79310288	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79244000-79288000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:79272200-79284400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:79272400-79286400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr15:79276400-79288600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:79276400-79309200	Weak transcription	Right Atrium	heart
6	chr15:79277400-79282000	Weak transcription	Brain Angular Gyrus	brain
7	chr15:79277600-79284000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:79278400-79290400	Enhancers	Fetal Intestine Small	intestine
9	chr15:79279400-79287000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:79279600-79281800	Enhancers	GM12878-XiMat	blood
11	chr15:79279600-79291000	Enhancers	Fetal Intestine Large	intestine
12	chr15:79279800-79282600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:79279800-79285600	Enhancers	HepG2	liver
14	chr15:79280000-79281200	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr15:79280000-79282000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:79280000-79282400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:79280000-79282400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:79280000-79282400	Enhancers	HMEC	breast
19	chr15:79280000-79282400	Enhancers	NHDF-Ad	bronchial
20	chr15:79280000-79282400	Enhancers	NHEK	skin
21	chr15:79280000-79283000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:79280000-79283800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr15:79280000-79286800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:79280200-79281200	Enhancers	Gastric	stomach
25	chr15:79280200-79281600	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr15:79280200-79281600	Enhancers	HUVEC	blood vessel
27	chr15:79280200-79282000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:79280200-79282400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:79280200-79282600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr15:79280200-79282800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr15:79280200-79282800	Enhancers	Adipose Nuclei	Adipose
32	chr15:79280200-79283200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr15:79280200-79285000	Enhancers	HSMM	muscle
34	chr15:79280200-79286000	Enhancers	HSMMtube	muscle
35	chr15:79280200-79286400	Enhancers	Placenta	Placenta
36	chr15:79280400-79281600	Enhancers	Brain Substantia Nigra	brain
37	chr15:79280400-79281600	Enhancers	Hela-S3	cervix
38	chr15:79280400-79281800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:79280400-79281800	Enhancers	Esophagus	oesophagus
40	chr15:79280400-79281800	Enhancers	Ovary	ovary
41	chr15:79280400-79281800	Enhancers	A549	lung
42	chr15:79280400-79282200	Enhancers	NHLF	lung
43	chr15:79280400-79282400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr15:79280400-79282600	Enhancers	NH-A	brain
45	chr15:79280400-79283000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:79280400-79283000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr15:79280400-79283200	Enhancers	Colon Smooth Muscle	Colon
48	chr15:79280400-79284400	Weak transcription	Small Intestine	intestine
49	chr15:79280600-79281400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:79280600-79281400	Weak transcription	Brain Hippocampus Middle	brain

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