Variant report

Variant	rs7651449
Chromosome Location	chr3:159480605-159480606
allele	G/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	SMARCB1	chr3:159480566-159483718	Hela-S3	cervix:	n/a	chr3:159483592-159483601
2	POLR2A	chr3:159480562-159484035	PFSK-1	brain:	n/a	n/a
3	CEBPB	chr3:159480064-159482341	Hela-S3	cervix:	n/a	n/a
4	EP300	chr3:159479975-159481767	A549	lung:	n/a	chr3:159481639-159481652 chr3:159480947-159480956
5	POLR2A	chr3:159478872-159485842	IMR90	lung:	n/a	n/a
6	POLR2A	chr3:159480551-159481771	Hela-S3	cervix:	n/a	n/a
7	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
8	SMARCC1	chr3:159479275-159481600	Hela-S3	cervix:	n/a	chr3:159479718-159479727
9	POLR2A	chr3:159480483-159482854	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:159480560-159483811	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:159480579-159482427	HCT-116	colon:	n/a	n/a
12	MXI1	chr3:159480081-159481644	Hela-S3	cervix:	n/a	n/a
13	SP1	chr3:159480548-159482516	A549	lung:	n/a	chr3:159481886-159481899 chr3:159481542-159481551 chr3:159481606-159481620 chr3:159481892-159481901 chr3:159481902-159481909 chr3:159482087-159482101 chr3:159481834-159481843 chr3:159482175-159482189 chr3:159481892-159481901 chr3:159481538-159481552 chr3:159481609-159481621 chr3:159481891-159481901 chr3:159482086-159482098 chr3:159482088-159482097 chr3:159481891-159481900
14	USF2	chr3:159479997-159481135	Hela-S3	cervix:	n/a	n/a
15	BRCA1	chr3:159479495-159481576	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr3:159479069-159484734	HUVEC	blood vessel:	n/a	n/a
17	MAX	chr3:159480585-159482561	A549	lung:	n/a	chr3:159481565-159481574
18	MXI1	chr3:159480603-159484814	IMR90	lung:	n/a	n/a
19	TFAP2C	chr3:159479888-159484192	Hela-S3	cervix:	n/a	chr3:159482066-159482081 chr3:159482088-159482103 chr3:159481475-159481490
20	GTF2F1	chr3:159480004-159481606	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:159480601-159483832	ProgFib	skin:	n/a	n/a
22	TCF12	chr3:159480443-159482492	ECC-1	luminal epithelium:	n/a	n/a
23	MAZ	chr3:159480542-159483866	Hela-S3	cervix:	n/a	chr3:159481565-159481574 chr3:159482995-159483005 chr3:159483043-159483053
24	RCOR1	chr3:159479354-159482527	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr3:159480493-159481732	ECC-1	luminal epithelium:	n/a	n/a
26	SP1	chr3:159480562-159482412	A549	lung:	n/a	chr3:159481886-159481899 chr3:159481542-159481551 chr3:159481606-159481620 chr3:159481892-159481901 chr3:159481902-159481909 chr3:159482087-159482101 chr3:159481834-159481843 chr3:159482175-159482189 chr3:159481892-159481901 chr3:159481538-159481552 chr3:159481609-159481621 chr3:159481891-159481901 chr3:159482086-159482098 chr3:159482088-159482097 chr3:159481891-159481900
27	TCF12	chr3:159479694-159483817	A549	lung:	n/a	chr3:159480036-159480043 chr3:159479977-159479986
28	RCOR1	chr3:159480472-159485057	IMR90	lung:	n/a	n/a
29	POLR2A	chr3:159480461-159484312	HUVEC	blood vessel:	n/a	n/a
30	RFX5	chr3:159480036-159481663	Hela-S3	cervix:	n/a	n/a
31	NFIC	chr3:159480571-159482453	ECC-1	luminal epithelium:	n/a	n/a
32	MAFK	chr3:159480073-159480936	Hela-S3	cervix:	n/a	n/a
33	MAX	chr3:159480569-159482436	ECC-1	luminal epithelium:	n/a	chr3:159481565-159481574
34	POLR2A	chr3:159480562-159484787	U87	brain:	n/a	n/a
35	POLR2A	chr3:159480371-159484211	HUVEC	blood vessel:	n/a	n/a
36	GATA3	chr3:159480550-159482495	A549	lung:	n/a	chr3:159481209-159481217
37	TBP	chr3:159480037-159481696	Hela-S3	cervix:	n/a	n/a
38	STAT3	chr3:159480566-159481013	MCF10A-Er-Src	breast:	n/a	chr3:159480982-159480994
39	REST	chr3:159480016-159481774	A549	lung:	n/a	chr3:159481516-159481529
40	ZKSCAN1	chr3:159480095-159481723	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr3:159480555-159482625	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr3:159480568-159484662	U87	brain:	n/a	n/a
43	GATA2	chr3:159480550-159481177	HUVEC	blood vessel:	n/a	n/a
44	EP300	chr3:159479860-159482393	ECC-1	luminal epithelium:	n/a	chr3:159482129-159482145 chr3:159481639-159481652 chr3:159480947-159480956
45	MAX	chr3:159479909-159483977	A549	lung:	n/a	chr3:159481565-159481574 chr3:159482995-159483005 chr3:159483043-159483053
46	FOS	chr3:159480446-159481631	HUVEC	blood vessel:	n/a	chr3:159481541-159481550
47	EGR1	chr3:159480584-159482411	HCT-116	colon:	n/a	chr3:159481120-159481129 chr3:159481542-159481552 chr3:159481631-159481644 chr3:159481812-159481827 chr3:159482089-159482102
48	CHD2	chr3:159480050-159483871	Hela-S3	cervix:	n/a	chr3:159480992-159481002
49	CHD1	chr3:159479850-159485380	IMR90	lung:	n/a	chr3:159480992-159481002
50	POLR2A	chr3:159479736-159481638	A549	lung:	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: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10440023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470474	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13314923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28695486	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4621369	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56786891	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6781743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015941	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015951	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015956	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015967	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017937	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017943	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017960	1.00[EUR][1000 genomes]
rs7612849	1.00[EUR][1000 genomes]
rs7615917	0.83[AMR][1000 genomes]
rs9811600	0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814058	1.00[EUR][1000 genomes]
rs9816506	0.83[AMR][1000 genomes]
rs9830331	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9832139	0.92[AMR][1000 genomes]
rs9845205	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845849	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846391	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846819	1.00[EUR][1000 genomes]
rs9850723	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853947	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853973	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9855171	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9872127	0.83[AMR][1000 genomes]
rs9877761	0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878860	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9880866	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159478800-159480800	Flanking Active TSS	A549	lung
2	chr3:159479200-159480800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:159479400-159481000	Flanking Active TSS	HUVEC	blood vessel
4	chr3:159479600-159480800	Enhancers	Lung	lung
5	chr3:159479600-159481000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:159479600-159481000	Flanking Active TSS	NHDF-Ad	bronchial
7	chr3:159479600-159481200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:159479600-159481200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:159479600-159481200	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr3:159479600-159481200	Flanking Active TSS	HSMM	muscle
11	chr3:159479600-159481200	Flanking Active TSS	NHEK	skin
12	chr3:159479600-159481400	Flanking Active TSS	HMEC	breast
13	chr3:159479800-159480800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:159479800-159480800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:159479800-159480800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:159479800-159481000	Flanking Active TSS	Osteobl	bone
17	chr3:159479800-159481200	Flanking Active TSS	HSMMtube	muscle
18	chr3:159480000-159481000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:159480000-159481000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:159480000-159481000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr3:159480000-159481400	Flanking Active TSS	NH-A	brain
22	chr3:159480000-159483200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
23	chr3:159480200-159481000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:159480200-159481000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:159480200-159481000	Flanking Active TSS	Fetal Heart	heart
26	chr3:159480200-159481000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:159480200-159481200	Flanking Active TSS	Hela-S3	cervix
28	chr3:159480400-159480800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:159480400-159480800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:159480400-159480800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:159480400-159480800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:159480400-159480800	Enhancers	Brain Germinal Matrix	brain
33	chr3:159480400-159480800	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr3:159480400-159480800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr3:159480400-159480800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
36	chr3:159480400-159481200	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr3:159480400-159481400	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr3:159480400-159483400	Active TSS	H1 Cell Line	embryonic stem cell
39	chr3:159480400-159483800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr3:159480400-159483800	Active TSS	H9 Cell Line	embryonic stem cell
41	chr3:159480400-159483800	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr3:159480400-159484200	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr3:159480600-159480800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:159480600-159480800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr3:159480600-159480800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:159480600-159480800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr3:159480600-159480800	Enhancers	Primary B cells from peripheral blood	blood
48	chr3:159480600-159480800	Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr3:159480600-159480800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
50	chr3:159480600-159480800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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