Variant report

Variant	rs62270376
Chromosome Location	chr3:159480523-159480524
allele	A/T
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	CEBPB	chr3:159480064-159482341	Hela-S3	cervix:	n/a	n/a
2	EP300	chr3:159479975-159481767	A549	lung:	n/a	chr3:159481639-159481652 chr3:159480947-159480956
3	POLR2A	chr3:159478872-159485842	IMR90	lung:	n/a	n/a
4	TEAD4	chr3:159479971-159480535	ECC-1	luminal epithelium:	n/a	n/a
5	SMC3	chr3:159479813-159484045	Hela-S3	cervix:	n/a	chr3:159481356-159481366 chr3:159481836-159481846 chr3:159482090-159482100 chr3:159482126-159482136 chr3:159480742-159480749 chr3:159481981-159481988
6	SMARCC1	chr3:159479275-159481600	Hela-S3	cervix:	n/a	chr3:159479718-159479727
7	POLR2A	chr3:159480483-159482854	H1-hESC	embryonic stem cell:	n/a	n/a
8	MXI1	chr3:159480081-159481644	Hela-S3	cervix:	n/a	n/a
9	USF2	chr3:159479997-159481135	Hela-S3	cervix:	n/a	n/a
10	BRCA1	chr3:159479495-159481576	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:159479069-159484734	HUVEC	blood vessel:	n/a	n/a
12	TEAD4	chr3:159479885-159480580	ECC-1	luminal epithelium:	n/a	n/a
13	TFAP2C	chr3:159479888-159484192	Hela-S3	cervix:	n/a	chr3:159482066-159482081 chr3:159482088-159482103 chr3:159481475-159481490
14	GTF2F1	chr3:159480004-159481606	Hela-S3	cervix:	n/a	n/a
15	TCF12	chr3:159480443-159482492	ECC-1	luminal epithelium:	n/a	n/a
16	RCOR1	chr3:159479354-159482527	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr3:159480493-159481732	ECC-1	luminal epithelium:	n/a	n/a
18	SP1	chr3:159479908-159480547	A549	lung:	n/a	chr3:159480055-159480062
19	TEAD4	chr3:159479965-159480525	A549	lung:	n/a	n/a
20	TCF12	chr3:159479694-159483817	A549	lung:	n/a	chr3:159480036-159480043 chr3:159479977-159479986
21	RCOR1	chr3:159480472-159485057	IMR90	lung:	n/a	n/a
22	POLR2A	chr3:159480461-159484312	HUVEC	blood vessel:	n/a	n/a
23	RFX5	chr3:159480036-159481663	Hela-S3	cervix:	n/a	n/a
24	MAFK	chr3:159480073-159480936	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr3:159480371-159484211	HUVEC	blood vessel:	n/a	n/a
26	SP1	chr3:159479867-159480530	A549	lung:	n/a	chr3:159480055-159480062
27	RAD21	chr3:159479968-159480543	A549	lung:	n/a	n/a
28	TBP	chr3:159480037-159481696	Hela-S3	cervix:	n/a	n/a
29	REST	chr3:159480016-159481774	A549	lung:	n/a	chr3:159481516-159481529
30	ZKSCAN1	chr3:159480095-159481723	Hela-S3	cervix:	n/a	n/a
31	EP300	chr3:159479860-159482393	ECC-1	luminal epithelium:	n/a	chr3:159482129-159482145 chr3:159481639-159481652 chr3:159480947-159480956
32	MAX	chr3:159479909-159483977	A549	lung:	n/a	chr3:159481565-159481574 chr3:159482995-159483005 chr3:159483043-159483053
33	FOS	chr3:159480446-159481631	HUVEC	blood vessel:	n/a	chr3:159481541-159481550
34	CHD2	chr3:159480050-159483871	Hela-S3	cervix:	n/a	chr3:159480992-159481002
35	CHD1	chr3:159479850-159485380	IMR90	lung:	n/a	chr3:159480992-159481002
36	POLR2A	chr3:159479736-159481638	A549	lung:	n/a	n/a
37	MAZ	chr3:159480063-159484869	IMR90	lung:	n/a	chr3:159481565-159481574 chr3:159482995-159483005 chr3:159483043-159483053
38	TCF12	chr3:159479856-159481764	ECC-1	luminal epithelium:	n/a	chr3:159480036-159480043 chr3:159479977-159479986
39	CTCF	chr3:159480420-159480570	AG10803	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:154041649..154042465-chr3:159480471..159481388,2	Hela-S3	cervix:
2	chr3:159379905..159381514-chr3:159477942..159480811,2	MCF-7	breast:

Variant related genes	Relation type
IQCJ-SCHIP1	TF binding region
ENSG00000174953	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16830774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1846130	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62270378	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62270380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62270382	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62270384	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62270385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62270386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62270388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62270391	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62270393	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62270394	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62270396	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62270398	0.84[EUR][1000 genomes]
rs62270399	0.84[EUR][1000 genomes]
rs62270402	0.84[EUR][1000 genomes]
rs6762494	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6762595	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6767193	0.84[EUR][1000 genomes]
rs6770054	0.94[EUR][1000 genomes]
rs6771235	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7637455	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	esv3335783	chr3:159480158-159484256	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3426837	chr3:159480283-159483031	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159450800-159480600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:159477000-159480600	Weak transcription	Fetal Brain Male	brain
3	chr3:159477600-159480600	Enhancers	Fetal Lung	lung
4	chr3:159478000-159480600	Enhancers	Liver	Liver
5	chr3:159478200-159480600	Enhancers	Fetal Kidney	kidney
6	chr3:159478800-159480600	Enhancers	Placenta	Placenta
7	chr3:159478800-159480600	Enhancers	Rectal Smooth Muscle	rectum
8	chr3:159478800-159480800	Flanking Active TSS	A549	lung
9	chr3:159479000-159480600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:159479000-159480600	Enhancers	Brain Anterior Caudate	brain
11	chr3:159479000-159480600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:159479000-159480600	Enhancers	Fetal Stomach	stomach
13	chr3:159479000-159480600	Enhancers	Left Ventricle	heart
14	chr3:159479000-159480600	Enhancers	NHLF	lung
15	chr3:159479200-159480600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:159479200-159480600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:159479200-159480600	Enhancers	Brain Angular Gyrus	brain
18	chr3:159479200-159480600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:159479200-159480600	Enhancers	Brain Hippocampus Middle	brain
20	chr3:159479200-159480800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:159479400-159480600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:159479400-159481000	Flanking Active TSS	HUVEC	blood vessel
23	chr3:159479600-159480600	Enhancers	Fetal Muscle Trunk	muscle
24	chr3:159479600-159480600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:159479600-159480600	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr3:159479600-159480800	Enhancers	Lung	lung
27	chr3:159479600-159481000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:159479600-159481000	Flanking Active TSS	NHDF-Ad	bronchial
29	chr3:159479600-159481200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:159479600-159481200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:159479600-159481200	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr3:159479600-159481200	Flanking Active TSS	HSMM	muscle
33	chr3:159479600-159481200	Flanking Active TSS	NHEK	skin
34	chr3:159479600-159481400	Flanking Active TSS	HMEC	breast
35	chr3:159479800-159480600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:159479800-159480600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:159479800-159480800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:159479800-159480800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr3:159479800-159480800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:159479800-159481000	Flanking Active TSS	Osteobl	bone
41	chr3:159479800-159481200	Flanking Active TSS	HSMMtube	muscle
42	chr3:159480000-159480600	Enhancers	Fetal Intestine Large	intestine
43	chr3:159480000-159480600	Active TSS	Right Ventricle	heart
44	chr3:159480000-159481000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr3:159480000-159481000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:159480000-159481000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr3:159480000-159481400	Flanking Active TSS	NH-A	brain
48	chr3:159480000-159483200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
49	chr3:159480200-159480600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr3:159480200-159480600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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