Variant report

Variant	rs28738778
Chromosome Location	chr15:79271725-79271726
allele	C/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	MTA3	chr15:79270733-79272504	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:79268732-79273709	GM12891	blood:	n/a	n/a
3	EBF1	chr15:79270842-79272413	GM12878	blood:	n/a	chr15:79270961-79270970 chr15:79270961-79270971
4	POLR2A	chr15:79271550-79271833	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:79270756-79272484	GM12892	blood:	n/a	n/a
6	ELF1	chr15:79270837-79271873	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:79271116-79272350	GM12892	blood:	n/a	n/a
8	POLR2A	chr15:79270861-79272400	GM19193	blood:	n/a	n/a
9	MAX	chr15:79271640-79272552	A549	lung:	n/a	chr15:79272112-79272122
10	NFIC	chr15:79271638-79272138	GM12878	blood:	n/a	n/a
11	CTCF	chr15:79271488-79272801	A549	lung:	n/a	n/a
12	TBL1XR1	chr15:79270977-79272410	GM12878	blood:	n/a	n/a
13	MYC	chr15:79271685-79272559	A549	lung:	n/a	chr15:79272112-79272122
14	POLR2A	chr15:79268888-79273418	GM12878	blood:	n/a	n/a
15	SMC3	chr15:79271083-79272456	GM12878	blood:	n/a	n/a
16	MTA3	chr15:79271335-79271917	GM12878	blood:	n/a	n/a
17	POLR2A	chr15:79270926-79272439	GM12878	blood:	n/a	n/a
18	EP300	chr15:79271444-79272057	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:79270840-79272689	GM12892	blood:	n/a	n/a
20	RUNX3	chr15:79271385-79272431	GM12878	blood:	n/a	n/a
21	NFIC	chr15:79271679-79272493	GM12878	blood:	n/a	n/a
22	WRNIP1	chr15:79271359-79272526	GM12878	blood:	n/a	n/a
23	RAD21	chr15:79271614-79272664	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr15:79271600-79271750	NB4	blood:	n/a	n/a
25	STAT5A	chr15:79271252-79272484	GM12878	blood:	n/a	n/a
26	ELK1	chr15:79271668-79272358	GM12878	blood:	n/a	n/a
27	MXI1	chr15:79271598-79272760	SK-N-SH	brain:	n/a	n/a
28	EBF1	chr15:79270838-79271754	GM12878	blood:	n/a	chr15:79270961-79270970 chr15:79270961-79270971
29	POLR2A	chr15:79270713-79272515	GM12892	blood:	n/a	n/a
30	POLR2A	chr15:79270875-79272437	GM18951	blood:	n/a	n/a
31	RELA	chr15:79271093-79272445	GM19193	blood:	n/a	n/a
32	POLR2A	chr15:79271445-79272411	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:79270754-79272517	GM12878	blood:	n/a	n/a
34	MAX	chr15:79271699-79272505	A549	lung:	n/a	chr15:79272112-79272122
35	POLR2A	chr15:79270858-79272371	GM15510	blood:	n/a	n/a
36	MAX	chr15:79271677-79272450	MCF-7	breast:	n/a	chr15:79272112-79272122
37	MAX	chr15:79271625-79272463	H1-hESC	embryonic stem cell:	n/a	chr15:79272112-79272122

No.	Distal block	Cell Line	Cell type
1	chr15:79242855..79244395-chr15:79271553..79274104,2	MCF-7	breast:
2	chr15:79271517..79274349-chr15:79274954..79277693,2	K562	blood:
3	chr15:79201766..79202756-chr15:79271684..79272710,8	MCF-7	breast:
4	chr15:79218320..79219259-chr15:79271509..79272622,7	MCF-7	breast:
5	chr15:79206090..79206967-chr15:79271525..79272450,5	MCF-7	breast:
6	chr15:79271475..79273812-chr15:79473082..79474740,2	MCF-7	breast:
7	chr15:79218551..79219226-chr15:79271642..79272206,2	MCF-7	breast:
8	chr15:79217200..79220348-chr15:79270743..79273551,3	MCF-7	breast:
9	chr15:79165092..79167959-chr15:79271269..79275481,5	MCF-7	breast:

Variant related genes	Relation type
RASGRF1	TF binding region
ENSG00000103811	Chromatin interaction
ENSG00000185787	Chromatin interaction
ENSG00000058335	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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28391216	1.00[EUR][1000 genomes]
rs28407629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28427472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28461937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464364	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501391	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501618	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28513164	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28516885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28546944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28547879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28549817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28557276	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28565526	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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28674868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28683537	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705105	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28709904	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28716558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28718997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28722773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920807	1.00[AFR][1000 genomes];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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79244000-79288000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:79261200-79280400	Weak transcription	Esophagus	oesophagus
3	chr15:79264200-79271800	Weak transcription	Brain Angular Gyrus	brain
4	chr15:79268200-79272400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr15:79268400-79272600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr15:79268800-79273200	Enhancers	Primary B cells from peripheral blood	blood
7	chr15:79269000-79272400	Enhancers	Primary B cells from cord blood	blood
8	chr15:79269000-79272400	Enhancers	Spleen	Spleen
9	chr15:79269200-79272400	Enhancers	HepG2	liver
10	chr15:79269800-79272200	Enhancers	Brain Cingulate Gyrus	brain
11	chr15:79270000-79271800	Weak transcription	Brain Anterior Caudate	brain
12	chr15:79270000-79271800	Weak transcription	Fetal Intestine Large	intestine
13	chr15:79270000-79278400	Weak transcription	Fetal Intestine Small	intestine
14	chr15:79270400-79271800	Weak transcription	K562	blood
15	chr15:79270400-79272000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:79270400-79274400	Weak transcription	HSMMtube	muscle
17	chr15:79270600-79271800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr15:79270800-79272800	Flanking Active TSS	GM12878-XiMat	blood
19	chr15:79270800-79274000	Enhancers	Fetal Muscle Trunk	muscle
20	chr15:79271000-79272200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:79271000-79272200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr15:79271000-79272200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:79271200-79272000	Active TSS	Duodenum Mucosa	Duodenum
24	chr15:79271200-79272200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:79271200-79272200	Enhancers	Right Ventricle	heart
26	chr15:79271200-79272400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr15:79271400-79272200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr15:79271400-79272200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:79271400-79272200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:79271400-79272200	Enhancers	Fetal Lung	lung
31	chr15:79271400-79272200	Enhancers	Ovary	ovary
32	chr15:79271400-79272200	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr15:79271400-79272200	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr15:79271400-79272400	Enhancers	Adipose Nuclei	Adipose
35	chr15:79271400-79272400	Enhancers	Brain Hippocampus Middle	brain
36	chr15:79271400-79272400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr15:79271400-79275600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:79271600-79271800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:79271600-79272200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:79271600-79272200	Enhancers	Brain Substantia Nigra	brain
41	chr15:79271600-79272200	Enhancers	Fetal Kidney	kidney
42	chr15:79271600-79272200	Enhancers	Placenta	Placenta
43	chr15:79271600-79272200	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr15:79271600-79272400	Enhancers	Fetal Muscle Leg	muscle
45	chr15:79271600-79272400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr15:79271600-79272400	Enhancers	HMEC	breast
47	chr15:79271600-79275800	Weak transcription	Lung	lung

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