Variant report

Variant	rs3784540
Chromosome Location	chr15:79219332-79219333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:79219167-79219705	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:79217212-79220767	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr15:79210927-79227564	K562	blood:	n/a	n/a
4	MTA3	chr15:79219093-79219637	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:79219261-79219574	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:79219231-79219812	GM12892	blood:	n/a	n/a
7	POLR2A	chr15:79218572-79220031	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:79217437-79220722	GM15510	blood:	n/a	n/a
9	SUZ12	chr15:79219289-79219754	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:79217371-79220785	K562	blood:	n/a	n/a
11	POLR2A	chr15:79219243-79219467	HepG2	liver:	n/a	n/a
12	POLR2A	chr15:79218498-79219998	H1-hESC	embryonic stem cell:	n/a	n/a
13	PML	chr15:79219140-79219785	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:79218873-79219493	HUVEC	blood vessel:	n/a	n/a
15	NFATC1	chr15:79218862-79219908	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:79217306-79227452	GM12892	blood:	n/a	n/a
17	POLR2A	chr15:79218209-79220623	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:79217247-79220366	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:79219282-79219815	GM12891	blood:	n/a	n/a
20	STAT5A	chr15:79217307-79219879	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:79219148-79220767	K562	blood:	n/a	n/a
22	POLR2A	chr15:79218317-79220545	GM12892	blood:	n/a	n/a
23	POLR2A	chr15:79217446-79220602	A549	lung:	n/a	n/a
24	POLR2A	chr15:79217342-79222654	GM12878	blood:	n/a	n/a
25	POLR2A	chr15:79219171-79220192	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:79211550-79222698	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:79210815-79222697	GM12891	blood:	n/a	n/a
28	POLR2A	chr15:79217356-79220698	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr15:79217378-79220689	GM19193	blood:	n/a	n/a
30	POLR2A	chr15:79218042-79220023	U87	brain:	n/a	n/a
31	POLR2A	chr15:79218505-79219790	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr15:79219187-79219628	K562	blood:	n/a	n/a
33	FOSL2	chr15:79219213-79220695	HepG2	liver:	n/a	n/a
34	BCL3	chr15:79219083-79219893	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:79219231-79219466	MCF-7	breast:	n/a	n/a
36	POLR2A	chr15:79219180-79219369	Hela-S3	cervix:	n/a	n/a
37	STAT5A	chr15:79219072-79219451	GM12878	blood:	n/a	n/a
38	POLR2A	chr15:79217530-79219636	K562	blood:	n/a	n/a
39	POLR2A	chr15:79219238-79219865	HepG2	liver:	n/a	n/a
40	POLR2A	chr15:79218024-79219853	SK-N-MC	brain:	n/a	n/a
41	POLR2A	chr15:79217326-79220672	GM18951	blood:	n/a	n/a
42	POLR2A	chr15:79218282-79220715	GM12892	blood:	n/a	n/a
43	POLR2A	chr15:79217480-79220739	GM19099	blood:	n/a	n/a
44	POLR2A	chr15:79219101-79219820	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr15:79217632-79220622	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr15:79219231-79220115	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:79217474-79220810	GM12892	blood:	n/a	n/a
48	POLR2A	chr15:79219277-79219417	A549	lung:	n/a	n/a
49	POLR2A	chr15:79219279-79219595	K562	blood:	n/a	n/a
50	SPI1	chr15:79219150-79219794	HL-60	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:79215592..79220788-chr15:79222055..79225592,6	MCF-7	breast:
2	chr15:79216646..79219513-chr15:79226461..79228629,2	MCF-7	breast:
3	chr15:79219205..79223895-chr15:79234790..79239038,6	MCF-7	breast:
4	chr15:79217200..79220348-chr15:79270743..79273551,3	MCF-7	breast:

No data

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

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10152868	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12440862	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970287	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2289691	0.82[ASN][1000 genomes]
rs2289695	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2289697	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289698	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289700	0.99[EUR][1000 genomes]
rs3784537	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58119858	1.00[EUR][1000 genomes]
rs60888706	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60944855	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7161986	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7163828	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182836	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73470389	1.00[EUR][1000 genomes]
rs8034542	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8039683	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302286	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3784540	CTSH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79178200-79219400	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr15:79190000-79222200	Strong transcription	Thymus	Thymus
3	chr15:79199800-79229400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:79203600-79231000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:79204800-79219600	Strong transcription	Fetal Brain Female	brain
6	chr15:79205400-79227800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:79205800-79223600	Weak transcription	Stomach Mucosa	stomach
8	chr15:79208200-79221800	Weak transcription	HMEC	breast
9	chr15:79208200-79223000	Weak transcription	Right Atrium	heart
10	chr15:79208400-79220400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:79208400-79221000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:79208600-79223000	Weak transcription	Hela-S3	cervix
13	chr15:79209400-79220200	Strong transcription	Fetal Thymus	thymus
14	chr15:79209600-79220200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:79209600-79220200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:79209600-79220600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:79209800-79220400	Strong transcription	Adipose Nuclei	Adipose
18	chr15:79209800-79225800	Strong transcription	Fetal Stomach	stomach
19	chr15:79210000-79226600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr15:79210000-79227200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr15:79210200-79219800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:79210200-79227000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:79210200-79228200	Strong transcription	GM12878-XiMat	blood
24	chr15:79210400-79220200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:79210400-79220400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:79210400-79220600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:79210400-79222200	Strong transcription	Liver	Liver
28	chr15:79210400-79226200	Strong transcription	Fetal Intestine Small	intestine
29	chr15:79210400-79228000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:79210400-79230200	Strong transcription	Fetal Intestine Large	intestine
31	chr15:79210600-79220200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:79211000-79219400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr15:79211600-79220600	Strong transcription	Primary T cells from cord blood	blood
34	chr15:79211600-79220600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:79212000-79222400	Strong transcription	Left Ventricle	heart
36	chr15:79212200-79226000	Weak transcription	Fetal Brain Male	brain
37	chr15:79212400-79220200	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:79213200-79220400	Strong transcription	Colon Smooth Muscle	Colon
39	chr15:79213400-79220600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:79213400-79220600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr15:79213400-79228400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:79213600-79219600	Strong transcription	Lung	lung
43	chr15:79213600-79219600	Strong transcription	Spleen	Spleen
44	chr15:79213600-79220200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:79213600-79220200	Strong transcription	HSMMtube	muscle
46	chr15:79213600-79220600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:79213600-79220600	Strong transcription	Aorta	Aorta
48	chr15:79213600-79220600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr15:79213600-79220600	Strong transcription	Rectal Smooth Muscle	rectum
50	chr15:79213600-79220600	Strong transcription	Right Ventricle	heart

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