Variant report

Variant	rs2289697
Chromosome Location	chr15:79221907-79221908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:79221063-79222441	A549	lung:	n/a	n/a
2	POLR2A	chr15:79220923-79222382	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:79210927-79227564	K562	blood:	n/a	n/a
4	POLR2A	chr15:79221210-79222676	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:79220572-79222607	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:79221837-79222225	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:79220950-79222543	GM18951	blood:	n/a	n/a
8	POLR2A	chr15:79221354-79222546	GM12892	blood:	n/a	n/a
9	POLR2A	chr15:79220977-79222584	GM19193	blood:	n/a	n/a
10	POLR2A	chr15:79220997-79222510	GM18526	blood:	n/a	n/a
11	POLR2A	chr15:79221860-79222012	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr15:79221786-79222186	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr15:79217306-79227452	GM12892	blood:	n/a	n/a
14	POLR2A	chr15:79221094-79222673	GM12892	blood:	n/a	n/a
15	POLR2A	chr15:79217342-79222654	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:79220854-79221923	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr15:79211550-79222698	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:79210815-79222697	GM12891	blood:	n/a	n/a
19	POLR2A	chr15:79220947-79222550	GM15510	blood:	n/a	n/a
20	MTA3	chr15:79221708-79222644	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:79220920-79222537	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:79221801-79222153	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr15:79221608-79221982	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr15:79220799-79221974	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr15:79221616-79222505	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:79221755-79222117	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:79221530-79222431	HepG2	liver:	n/a	n/a
28	POLR2A	chr15:79220890-79222657	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:79217215-79222665	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr15:79217321-79222679	GM18505	blood:	n/a	n/a
31	POLR2A	chr15:79221115-79222209	HepG2	liver:	n/a	n/a
32	POLR2A	chr15:79221621-79222666	HepG2	liver:	n/a	n/a
33	POLR2A	chr15:79217362-79222442	K562	blood:	n/a	n/a
34	POLR2A	chr15:79220926-79222491	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:79215921..79218148-chr15:79221781..79223713,2	MCF-7	breast:
2	chr15:79221142..79223357-chr15:79270700..79272228,2	K562	blood:
3	chr15:79220618..79223351-chr15:79275432..79277828,3	K562	blood:
4	chr15:79221080..79223572-chr15:79328024..79330400,2	MCF-7	breast:
5	chr15:79221775..79223364-chr15:79294791..79297170,2	MCF-7	breast:
6	chr15:79219384..79222077-chr15:79237429..79239448,2	MCF-7	breast:
7	chr15:79211630..79213704-chr15:79221735..79223665,2	K562	blood:
8	chr15:79221332..79223265-chr15:79228194..79229994,2	MCF-7	breast:
9	chr15:79219205..79223895-chr15:79234790..79239038,6	MCF-7	breast:
10	chr15:79220482..79222111-chr15:79292818..79294616,2	MCF-7	breast:
11	chr15:79221168..79222988-chr15:79241006..79242698,2	MCF-7	breast:
12	chr15:79164488..79167001-chr15:79221221..79222994,2	K562	blood:
13	chr15:79206363..79206930-chr15:79221801..79222652,2	MCF-7	breast:

No data

Variant related genes	Relation type
CTSH	TF binding region
ENSG00000185787	Chromatin interaction
ENSG00000103811	Chromatin interaction
ENSG00000177699	Chromatin interaction
ENSG00000058335	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10152868	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12440862	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12441725	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16970287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16970344	0.83[JPT][hapmap]
rs2289695	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2289698	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289700	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3784537	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784538	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784540	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3825931	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58119858	0.99[EUR][1000 genomes]
rs60888706	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60944855	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7161986	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7163828	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182836	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73470389	0.99[EUR][1000 genomes]
rs8034542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039683	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9302286	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2289697	CSK	cis	cerebellum	SCAN
rs2289697	MORF4L1	cis	parietal	SCAN
rs2289697	CTSH	Cis_1M	lymphoblastoid	RTeQTL
rs2289697	C15orf17	cis	cerebellum	SCAN
rs2289697	MORF4L1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79190000-79222200	Strong transcription	Thymus	Thymus
2	chr15:79199800-79229400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:79203600-79231000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:79205400-79227800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:79205800-79223600	Weak transcription	Stomach Mucosa	stomach
6	chr15:79208200-79223000	Weak transcription	Right Atrium	heart
7	chr15:79208600-79223000	Weak transcription	Hela-S3	cervix
8	chr15:79209800-79225800	Strong transcription	Fetal Stomach	stomach
9	chr15:79210000-79226600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr15:79210000-79227200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr15:79210200-79227000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:79210200-79228200	Strong transcription	GM12878-XiMat	blood
13	chr15:79210400-79222200	Strong transcription	Liver	Liver
14	chr15:79210400-79226200	Strong transcription	Fetal Intestine Small	intestine
15	chr15:79210400-79228000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:79210400-79230200	Strong transcription	Fetal Intestine Large	intestine
17	chr15:79212000-79222400	Strong transcription	Left Ventricle	heart
18	chr15:79212200-79226000	Weak transcription	Fetal Brain Male	brain
19	chr15:79213400-79228400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:79213600-79222200	Strong transcription	Pancreas	Pancrea
21	chr15:79214600-79223000	Weak transcription	NHDF-Ad	bronchial
22	chr15:79214600-79229400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:79214800-79223200	Weak transcription	Psoas Muscle	Psoas
24	chr15:79215200-79223000	Weak transcription	A549	lung
25	chr15:79215400-79222200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:79215400-79222200	Weak transcription	Osteobl	bone
27	chr15:79215400-79223400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:79215400-79233200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:79215400-79236600	Weak transcription	Small Intestine	intestine
30	chr15:79215600-79222000	Weak transcription	NHEK	skin
31	chr15:79215600-79222200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:79215600-79223000	Weak transcription	NH-A	brain
33	chr15:79215600-79229400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:79215600-79232800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:79215800-79229600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:79216000-79223000	Weak transcription	Fetal Lung	lung
37	chr15:79216000-79223000	Weak transcription	HUVEC	blood vessel
38	chr15:79217200-79229400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:79218200-79222400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr15:79218400-79222200	Genic enhancers	Primary monocytes fromperipheralblood	blood
41	chr15:79218400-79222200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:79218400-79223000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:79218400-79223600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:79219200-79222000	Weak transcription	Brain Germinal Matrix	brain
45	chr15:79219400-79229400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:79219400-79229600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:79219600-79225800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:79219600-79226400	Weak transcription	Fetal Brain Female	brain
49	chr15:79219600-79236200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:79219800-79226000	Weak transcription	Fetal Kidney	kidney

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