Variant report

Variant	rs16858483
Chromosome Location	chr3:146262399-146262400
allele	A/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	POLR2A	chr3:146262040-146262748	GM10847	blood:	n/a	n/a
2	MAX	chr3:146262059-146262732	H1-hESC	embryonic stem cell:	n/a	n/a
3	PAX5	chr3:146262176-146262642	GM12878	blood:	n/a	n/a
4	STAT3	chr3:146262256-146262825	Hela-S3	cervix:	n/a	chr3:146262365-146262376 chr3:146262565-146262577
5	HA-E2F1	chr3:146262028-146262676	Hela-S3	cervix:	n/a	chr3:146262203-146262215 chr3:146262476-146262487
6	HMGN3	chr3:146261924-146262770	K562	blood:	n/a	n/a
7	ELF1	chr3:146262133-146262713	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:146262120-146262907	HCT-116	colon:	n/a	n/a
9	PML	chr3:146262052-146262847	K562	blood:	n/a	chr3:146262234-146262242
10	POLR2A	chr3:146261878-146262827	K562	blood:	n/a	n/a
11	UBTF	chr3:146261236-146262874	K562	blood:	n/a	n/a
12	MTA3	chr3:146262081-146262701	GM12878	blood:	n/a	n/a
13	IRF1	chr3:146262146-146262836	K562	blood:	n/a	n/a
14	POLR2A	chr3:146262070-146262564	GM12892	blood:	n/a	n/a
15	E2F4	chr3:146262328-146262596	GM12878	blood:	n/a	chr3:146262475-146262486
16	YY1	chr3:146262165-146262529	HepG2	liver:	n/a	n/a
17	IRF4	chr3:146262143-146262609	GM12878	blood:	n/a	n/a
18	CEBPD	chr3:146262093-146262521	HepG2	liver:	n/a	n/a
19	SIN3AK20	chr3:146262083-146262621	A549	lung:	n/a	n/a
20	ZBTB33	chr3:146262282-146262592	K562	blood:	n/a	n/a
21	MAX	chr3:146261975-146262692	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:146262129-146262827	K562	blood:	n/a	n/a
23	TCF3	chr3:146262066-146262545	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:146260709-146263251	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr3:146260780-146262889	HUVEC	blood vessel:	n/a	n/a
26	TAF1	chr3:146261975-146262833	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr3:146261913-146262911	K562	blood:	n/a	n/a
28	FOS	chr3:146262260-146262856	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr3:146262157-146262588	GM12892	blood:	n/a	n/a
30	MYC	chr3:146262036-146263141	K562	blood:	n/a	n/a
31	POLR2A	chr3:146262180-146262557	A549	lung:	n/a	n/a
32	SP1	chr3:146262121-146262864	A549	lung:	n/a	chr3:146262563-146262572 chr3:146262562-146262574 chr3:146262562-146262574 chr3:146262564-146262573 chr3:146262563-146262577
33	MAZ	chr3:146261933-146262864	IMR90	lung:	n/a	n/a
34	SIN3AK20	chr3:146261902-146262866	MCF-7	breast:	n/a	n/a
35	POLR2A	chr3:146261980-146262619	GM12892	blood:	n/a	n/a
36	RFX5	chr3:146262170-146262473	HepG2	liver:	n/a	n/a
37	POLR2A	chr3:146261219-146262877	Hela-S3	cervix:	n/a	n/a
38	TAF1	chr3:146261960-146262901	A549	lung:	n/a	n/a
39	E2F6	chr3:146262058-146262681	K562	blood:	n/a	chr3:146262475-146262486 chr3:146262203-146262215
40	E2F6	chr3:146261957-146262935	A549	lung:	n/a	chr3:146262475-146262486 chr3:146262203-146262215 chr3:146262816-146262833
41	MAX	chr3:146261917-146262830	ECC-1	luminal epithelium:	n/a	n/a
42	SPI1	chr3:146262079-146262797	GM12891	blood:	n/a	n/a
43	E2F4	chr3:146261959-146263002	MCF10A-Er-Src	breast:	n/a	chr3:146262203-146262215 chr3:146262475-146262486 chr3:146262816-146262833
44	GTF2B	chr3:146262223-146262780	K562	blood:	n/a	n/a
45	POLR2A	chr3:146261693-146262886	K562	blood:	n/a	n/a
46	POLR2A	chr3:146261542-146262714	GM12878	blood:	n/a	n/a
47	MYC	chr3:146262063-146262904	K562	blood:	n/a	n/a
48	MAZ	chr3:146262120-146262792	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:146260810-146263078	GM19099	blood:	n/a	n/a
50	POLR2A	chr3:146260743-146263324	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:146262351..146263155-chr6:26216981..26217771,2	Hela-S3	cervix:
2	chr1:28974737..28975470-chr3:146262061..146262905,2	HCT-116	colon:
3	chr3:146254115..146256698-chr3:146261297..146263941,3	MCF-7	breast:
4	chr3:146261960..146262783-chr8:98787677..98788425,2	Hela-S3	cervix:
5	chr3:146234146..146236591-chr3:146261590..146264248,2	K562	blood:
6	chr3:146251866..146257697-chr3:146260468..146262994,8	MCF-7	breast:
7	chr2:170550671..170551359-chr3:146261829..146262448,2	Hela-S3	cervix:
8	chr2:74425544..74426237-chr3:146262234..146262977,2	HCT-116	colon:
9	chr3:146262237..146263074-chr5:33440580..33441428,2	Hela-S3	cervix:

Variant related genes	Relation type
PLSCR1	TF binding region
ENSG00000188313	Chromatin interaction
ENSG00000249572	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000104341	Chromatin interaction
ENSG00000113407	Chromatin interaction
ENSG00000213160	Chromatin interaction
ENSG00000144362	Chromatin interaction
ENSG00000154479	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000168274	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12107687	1.00[AMR][1000 genomes]
rs16858513	1.00[AMR][1000 genomes]
rs16858523	1.00[AMR][1000 genomes]
rs16858568	1.00[AMR][1000 genomes]
rs16858582	1.00[AMR][1000 genomes]
rs28429720	1.00[AMR][1000 genomes]
rs41414448	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs4615047	1.00[AMR][1000 genomes]
rs55796696	1.00[AMR][1000 genomes]
rs6768067	1.00[AMR][1000 genomes]
rs73865809	1.00[AMR][1000 genomes]
rs73865812	1.00[AMR][1000 genomes]
rs73865817	1.00[AMR][1000 genomes]
rs73867434	1.00[AMR][1000 genomes]
rs73867436	1.00[AMR][1000 genomes]
rs73867437	1.00[AMR][1000 genomes]
rs73867446	1.00[AMR][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	esv2496437	chr3:146186902-146262961	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1014493	chr3:146255594-146288414	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146258000-146263200	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr3:146258400-146263200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:146258800-146263000	Active TSS	Brain Anterior Caudate	brain
4	chr3:146258800-146263000	Active TSS	Ovary	ovary
5	chr3:146259200-146262800	Active TSS	Brain Hippocampus Middle	brain
6	chr3:146259200-146263200	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr3:146259200-146263200	Active TSS	Right Ventricle	heart
8	chr3:146259400-146263000	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:146259600-146262800	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr3:146259600-146263000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:146259600-146263000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:146259800-146262800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:146259800-146262800	Active TSS	Psoas Muscle	Psoas
14	chr3:146259800-146263000	Active TSS	Fetal Muscle Leg	muscle
15	chr3:146259800-146263200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:146259800-146263200	Active TSS	Colonic Mucosa	Colon
17	chr3:146260000-146263000	Active TSS	Liver	Liver
18	chr3:146260000-146263000	Active TSS	Fetal Stomach	stomach
19	chr3:146260000-146263200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr3:146260000-146263200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:146260200-146262800	Active TSS	Brain Angular Gyrus	brain
22	chr3:146260200-146262800	Active TSS	Pancreas	Pancrea
23	chr3:146260200-146262800	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr3:146260200-146263000	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr3:146260200-146263000	Active TSS	GM12878-XiMat	blood
26	chr3:146260200-146263000	Active TSS	Hela-S3	cervix
27	chr3:146260200-146263200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:146260400-146263000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:146260400-146263000	Active TSS	Fetal Intestine Large	intestine
30	chr3:146260400-146263000	Active TSS	Fetal Intestine Small	intestine
31	chr3:146260400-146263000	Active TSS	Rectal Smooth Muscle	rectum
32	chr3:146260600-146262400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:146260600-146263000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr3:146260800-146262800	Active TSS	Brain Substantia Nigra	brain
35	chr3:146260800-146262800	Active TSS	Gastric	stomach
36	chr3:146260800-146262800	Active TSS	Left Ventricle	heart
37	chr3:146260800-146262800	Active TSS	Lung	lung
38	chr3:146260800-146262800	Active TSS	Stomach Mucosa	stomach
39	chr3:146260800-146263000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr3:146260800-146263000	Active TSS	Placenta	Placenta
41	chr3:146260800-146263000	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr3:146260800-146263000	Active TSS	Thymus	Thymus
43	chr3:146260800-146263000	Active TSS	HSMMtube	muscle
44	chr3:146260800-146263200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:146260800-146263400	Active TSS	HSMM	muscle
46	chr3:146261000-146262800	Active TSS	Aorta	Aorta
47	chr3:146261000-146262800	Active TSS	Esophagus	oesophagus
48	chr3:146261000-146262800	Active TSS	Small Intestine	intestine
49	chr3:146261000-146263000	Active TSS	H9 Cell Line	embryonic stem cell
50	chr3:146261000-146263200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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