Variant report

Variant	rs7611573
Chromosome Location	chr3:160167277-160167278
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	SIN3AK20	chr3:160167178-160167672	A549	lung:	n/a	n/a
2	POLR2A	chr3:160166631-160168726	PBDE	blood:	n/a	n/a
3	MYC	chr3:160166930-160168286	K562	blood:	n/a	n/a
4	YY1	chr3:160166904-160167994	GM12878	blood:	n/a	chr3:160167122-160167130 chr3:160167123-160167133
5	BHLHE40	chr3:160166978-160168385	K562	blood:	n/a	chr3:160167198-160167214
6	NRF1	chr3:160167241-160167888	H1-hESC	embryonic stem cell:	n/a	chr3:160167654-160167668 chr3:160167657-160167668 chr3:160167798-160167812 chr3:160167657-160167671 chr3:160167657-160167668
7	TBP	chr3:160166808-160167654	Hela-S3	cervix:	n/a	n/a
8	JUN	chr3:160167195-160167576	H1-hESC	embryonic stem cell:	n/a	chr3:160167499-160167507
9	E2F6	chr3:160167276-160168142	A549	lung:	n/a	chr3:160167802-160167811 chr3:160168014-160168025 chr3:160168015-160168030 chr3:160168014-160168025 chr3:160167658-160167667 chr3:160168014-160168025
10	BCL3	chr3:160166946-160167789	A549	lung:	n/a	n/a
11	HDAC2	chr3:160166902-160168102	MCF-7	breast:	n/a	n/a
12	TCF12	chr3:160166824-160167979	ECC-1	luminal epithelium:	n/a	n/a
13	PML	chr3:160166789-160168418	K562	blood:	n/a	n/a
14	CEBPB	chr3:160166735-160167443	A549	lung:	n/a	n/a
15	POLR2A	chr3:160166912-160168340	Raji	blood:	n/a	n/a
16	YY1	chr3:160166861-160167918	SK-N-SH_RA	brain:	n/a	chr3:160167122-160167130 chr3:160167123-160167133
17	HEY1	chr3:160166688-160168801	K562	blood:	n/a	chr3:160167195-160167210
18	FOXM1	chr3:160167047-160168291	MCF-7	breast:	n/a	n/a
19	POLR2A	chr3:160167128-160167689	SK-N-SH	brain:	n/a	n/a
20	TAF1	chr3:160166916-160168375	H1-hESC	embryonic stem cell:	n/a	n/a
21	RCOR1	chr3:160166966-160167479	HepG2	liver:	n/a	n/a
22	MAX	chr3:160166939-160168100	ECC-1	luminal epithelium:	n/a	n/a
23	TCF7L2	chr3:160167118-160168011	HCT-116	colon:	n/a	n/a
24	POLR2A	chr3:160166848-160168419	GM12878	blood:	n/a	n/a
25	RCOR1	chr3:160166614-160168268	K562	blood:	n/a	n/a
26	TAF1	chr3:160167174-160167495	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr3:160167038-160168183	MCF-7	breast:	n/a	n/a
28	CTCF	chr3:160167266-160167303	Fibrobl	skin:	n/a	n/a
29	CTCF	chr3:160167160-160167310	K562	blood:	n/a	n/a
30	SETDB1	chr3:160166750-160168276	U2OS	brain:	n/a	chr3:160167658-160167667
31	FOXP2	chr3:160167182-160167871	PFSK-1	brain:	n/a	n/a
32	UBTF	chr3:160166862-160168424	K562	blood:	n/a	n/a
33	POLR2A	chr3:160166966-160167939	MCF-7	breast:	n/a	n/a
34	POLR2A	chr3:160167021-160168906	K562	blood:	n/a	n/a
35	EP300	chr3:160167161-160168359	GM12878	blood:	n/a	chr3:160168160-160168170
36	SIN3AK20	chr3:160166811-160167732	K562	blood:	n/a	n/a
37	ELF1	chr3:160167203-160168270	K562	blood:	n/a	chr3:160168139-160168151
38	POLR2A	chr3:160166802-160168137	GM12892	blood:	n/a	n/a
39	SMC3	chr3:160167092-160167600	Hela-S3	cervix:	n/a	chr3:160167394-160167404
40	ZEB1	chr3:160167024-160167949	GM12878	blood:	n/a	n/a
41	IRF1	chr3:160166583-160168714	K562	blood:	n/a	chr3:160167587-160167601 chr3:160168025-160168039 chr3:160168457-160168467
42	MYC	chr3:160167093-160168316	K562	blood:	n/a	n/a
43	RAD21	chr3:160166885-160167599	A549	lung:	n/a	chr3:160167552-160167566 chr3:160167349-160167358 chr3:160167394-160167404
44	CTCF	chr3:160166679-160168194	K562	blood:	n/a	n/a
45	MYC	chr3:160166511-160168056	A549	lung:	n/a	n/a
46	POLR2A	chr3:160166855-160167829	GM12892	blood:	n/a	n/a
47	POLR2A	chr3:160166840-160168551	GM12878	blood:	n/a	n/a
48	MAX	chr3:160167209-160167707	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr3:160166810-160168302	GM18505	blood:	n/a	n/a
50	PML	chr3:160166702-160168136	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160121669..160124122-chr3:160164375..160167615,4	MCF-7	breast:
2	chr3:160099375..160102379-chr3:160166288..160168879,3	MCF-7	breast:
3	chr3:160165801..160167391-chr3:160284829..160286413,2	K562	blood:
4	chr1:31538268..31538938-chr3:160167004..160167772,2	HCT-116	colon:
5	chr3:160116116..160127665-chr3:160158037..160169627,42	K562	blood:
6	chr3:160128237..160130777-chr3:160166954..160168598,2	K562	blood:
7	chr3:160131935..160134663-chr3:160164828..160167325,4	K562	blood:
8	chr3:160167035..160169821-chr3:160232708..160234646,2	K562	blood:
9	chr3:160166147..160168803-chr3:160282163..160283900,2	MCF-7	breast:
10	chr3:160166836..160169216-chr3:161090028..161092220,2	MCF-7	breast:
11	chr3:160164471..160170330-chr3:160281681..160284179,8	K562	blood:
12	chr3:160165891..160168986-chr3:160283501..160286413,4	K562	blood:
13	chr3:160116116..160124648-chr3:160162504..160168767,20	K562	blood:

Variant related genes	Relation type
ENSG00000244009	TF binding region
TRIM59	TF binding region
ENSG00000207779	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000198987	Chromatin interaction
ENSG00000134644	Chromatin interaction
ENSG00000238741	Chromatin interaction
ENSG00000113810	Chromatin interaction
ENSG00000068885	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2015054	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2015065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3773371	0.82[LWK][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs59700052	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60304551	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60703878	0.85[AFR][1000 genomes]
rs60824140	1.00[AMR][1000 genomes]
rs6441307	0.87[YRI][hapmap]
rs6764107	0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6772987	0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6787795	0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap]
rs68069205	0.89[AFR][1000 genomes]
rs7611148	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7631284	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160164600-160167800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:160164600-160168200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:160164800-160168000	Active TSS	NHLF	lung
4	chr3:160164800-160168200	Active TSS	K562	blood
5	chr3:160164800-160169000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:160165000-160169000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr3:160165200-160167800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:160165200-160167800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:160165200-160167800	Active TSS	HMEC	breast
10	chr3:160165200-160167800	Active TSS	NHDF-Ad	bronchial
11	chr3:160165200-160168200	Active TSS	Brain Germinal Matrix	brain
12	chr3:160165400-160167600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:160165400-160167800	Active TSS	HSMMtube	muscle
14	chr3:160165400-160168000	Active TSS	Aorta	Aorta
15	chr3:160165400-160168200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:160165400-160168200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:160165400-160169000	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr3:160165600-160167600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:160165600-160167800	Active TSS	Fetal Thymus	thymus
20	chr3:160165600-160167800	Active TSS	GM12878-XiMat	blood
21	chr3:160165600-160167800	Active TSS	NH-A	brain
22	chr3:160165600-160168000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:160165600-160168600	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr3:160165800-160168000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr3:160165800-160168400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:160166000-160167400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
27	chr3:160166000-160167800	Active TSS	Fetal Stomach	stomach
28	chr3:160166000-160167800	Active TSS	Thymus	Thymus
29	chr3:160166000-160168000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr3:160166000-160168200	Active TSS	Fetal Brain Female	brain
31	chr3:160166000-160168200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr3:160166000-160168600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr3:160166200-160167400	Active TSS	Fetal Brain Male	brain
34	chr3:160166200-160167800	Active TSS	Fetal Muscle Leg	muscle
35	chr3:160166200-160168200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:160166200-160168200	Active TSS	Placenta Amnion	Placenta Amnion
37	chr3:160166200-160168200	Active TSS	HSMM	muscle
38	chr3:160166200-160168400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:160166200-160168400	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr3:160166200-160168400	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr3:160166200-160168400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr3:160166200-160168400	Active TSS	Duodenum Mucosa	Duodenum
43	chr3:160166200-160168600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr3:160166400-160167800	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr3:160166400-160167800	Active TSS	Muscle Satellite Cultured Cells	--
46	chr3:160166400-160167800	Active TSS	Fetal Intestine Large	intestine
47	chr3:160166400-160167800	Active TSS	Fetal Intestine Small	intestine
48	chr3:160166400-160167800	Active TSS	A549	lung
49	chr3:160166400-160167800	Active TSS	HUVEC	blood vessel
50	chr3:160166400-160167800	Active TSS	Osteobl	bone

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