Variant report

Variant	rs689626
Chromosome Location	chr15:41149765-41149766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41148610..41153040-chr15:41153153..41159814,9	MCF-7	breast:
2	chr15:41030818..41032817-chr15:41149511..41151476,2	K562	blood:
3	chr15:41148671..41154287-chr15:41183537..41188403,13	MCF-7	breast:
4	chr15:41148391..41150317-chr15:41198254..41199827,2	K562	blood:
5	chr15:41103905..41106369-chr15:41148589..41150248,2	MCF-7	breast:
6	chr15:41140669..41146997-chr15:41148125..41153622,6	K562	blood:
7	chr15:41114945..41117610-chr15:41148637..41150372,2	MCF-7	breast:
8	chr15:41148526..41152420-chr15:41165640..41167925,3	K562	blood:
9	chr15:41149375..41150782-chr15:41185730..41187681,17	K562	blood:
10	chr15:41149480..41150541-chr15:41183744..41186792,17	MCF-7	breast:
11	chr15:41106395..41107951-chr15:41148998..41150842,2	K562	blood:
12	chr15:41137274..41141358-chr15:41148658..41151865,7	MCF-7	breast:
13	chr15:41077350..41078135-chr15:41149764..41150368,2	MCF-7	breast:
14	chr15:41149030..41159900-chr15:41180834..41187281,18	MCF-7	breast:
15	chr15:41147027..41152625-chr15:41184304..41188925,8	K562	blood:
16	chr15:41147225..41150329-chr15:41164541..41167398,4	K562	blood:
17	chr15:41148170..41150962-chr15:41183690..41186569,3	K562	blood:
18	chr15:41135227..41137674-chr15:41148810..41150815,2	K562	blood:
19	chr15:41149586..41150132-chr15:41314305..41314932,2	K562	blood:
20	chr15:41148133..41159834-chr15:41169228..41175193,12	MCF-7	breast:
21	chr15:41149235..41151054-chr15:41178496..41180499,2	MCF-7	breast:
22	chr15:41149182..41150445-chr15:41186035..41187095,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261183	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000264256	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000104142	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1049598	1.00[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs17649	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs3736287	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs4924508	0.93[CEU][hapmap]
rs643875	0.93[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659232	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690458	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690660	1.00[CHD][hapmap]
rs8028552	0.84[ASW][hapmap];0.93[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.89[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	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs689626	MGA	cis	cerebellum	SCAN
rs689626	RP11-111A22.1	cis	Artery Tibial	GTEx
rs689626	NUSAP1	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41137400-41152200	Weak transcription	Small Intestine	intestine
2	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
3	chr15:41140000-41149800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr15:41140000-41149800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr15:41140000-41150400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:41140200-41149800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:41140200-41150000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:41140400-41151200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:41140600-41150000	Weak transcription	Fetal Kidney	kidney
10	chr15:41140600-41151600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:41141200-41152600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:41141800-41149800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:41142000-41149800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:41144800-41149800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:41146600-41154200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:41147000-41149800	Weak transcription	Primary B cells from cord blood	blood
17	chr15:41147600-41151400	Genic enhancers	Rectal Mucosa Donor 29	rectum
18	chr15:41147800-41151600	Genic enhancers	Rectal Mucosa Donor 31	rectum
19	chr15:41148000-41150400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:41148200-41151600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:41148400-41151400	Genic enhancers	Duodenum Mucosa	Duodenum
22	chr15:41148400-41151800	Genic enhancers	Fetal Intestine Small	intestine
23	chr15:41148600-41149800	Genic enhancers	Placenta	Placenta
24	chr15:41148600-41149800	Genic enhancers	Gastric	stomach
25	chr15:41148600-41149800	Genic enhancers	Stomach Mucosa	stomach
26	chr15:41148600-41151600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr15:41148800-41149800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:41148800-41150400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:41148800-41150600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:41149000-41149800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr15:41149000-41150000	Genic enhancers	Fetal Intestine Large	intestine
32	chr15:41149000-41150200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
33	chr15:41149000-41150400	Enhancers	Colonic Mucosa	Colon
34	chr15:41149000-41154400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:41149200-41150400	Enhancers	Brain Cingulate Gyrus	brain
36	chr15:41149200-41151600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:41149200-41151600	Enhancers	Fetal Thymus	thymus
38	chr15:41149400-41149800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:41149400-41149800	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:41149400-41149800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:41149400-41149800	Enhancers	Brain Angular Gyrus	brain
42	chr15:41149400-41150000	Enhancers	HMEC	breast
43	chr15:41149400-41150000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr15:41149400-41150200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:41149400-41150200	Enhancers	Fetal Lung	lung
46	chr15:41149400-41150400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:41149400-41150400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr15:41149400-41150400	Flanking Active TSS	HepG2	liver
49	chr15:41149400-41150400	Genic enhancers	NHEK	skin
50	chr15:41149400-41150600	Enhancers	Placenta Amnion	Placenta Amnion

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