Variant report

Variant	rs9871045
Chromosome Location	chr3:179370599-179370600
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	chr3:179370232-179372454	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:179370265-179371759	HL-60	blood:	n/a	n/a
3	REST	chr3:179370390-179370734	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:179370317-179371626	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr3:179370196-179370685	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF7L2	chr3:179370303-179370768	Hela-S3	cervix:	n/a	n/a
7	ZBTB7A	chr3:179370506-179370893	HepG2	liver:	n/a	chr3:179370729-179370738
8	MEF2A	chr3:179370356-179370916	GM12878	blood:	n/a	chr3:179370810-179370821 chr3:179370811-179370820 chr3:179370808-179370823
9	FOXM1	chr3:179370057-179370931	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr3:179370309-179371625	ECC-1	luminal epithelium:	n/a	n/a
11	CTCF	chr3:179370560-179370710	AG04450	lung:	n/a	n/a
12	POLR2A	chr3:179370303-179371629	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:179370420-179371596	MCF-7	breast:	n/a	n/a
14	MXI1	chr3:179370317-179370733	Hela-S3	cervix:	n/a	n/a
15	SIN3A	chr3:179370381-179371712	GM12878	blood:	n/a	chr3:179371520-179371531
16	POLR2A	chr3:179370328-179371691	NB4	blood:	n/a	n/a
17	POLR2A	chr3:179370247-179371543	MCF-7	breast:	n/a	n/a
18	MAX	chr3:179370094-179372626	HCT-116	colon:	n/a	chr3:179372121-179372130
19	GTF2F1	chr3:179370396-179370679	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr3:179370392-179371528	Hela-S3	cervix:	n/a	n/a
21	RUNX3	chr3:179370072-179371843	GM12878	blood:	n/a	n/a
22	CEBPB	chr3:179370243-179370639	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr3:179370248-179371478	GM12878	blood:	n/a	n/a
24	MYBL2	chr3:179370257-179370858	HepG2	liver:	n/a	n/a
25	MAX	chr3:179370205-179370951	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr3:179370304-179371660	GM18951	blood:	n/a	n/a
27	TAF1	chr3:179370461-179371472	HepG2	liver:	n/a	n/a
28	MAX	chr3:179370134-179371743	A549	lung:	n/a	n/a
29	SIN3AK20	chr3:179370276-179371736	SK-N-SH	brain:	n/a	n/a
30	YY1	chr3:179370529-179371425	GM12891	blood:	n/a	chr3:179370761-179370772
31	SIN3AK20	chr3:179370118-179371808	MCF-7	breast:	n/a	n/a
32	POLR2A	chr3:179370251-179372409	IMR90	lung:	n/a	n/a
33	MAX	chr3:179370541-179371529	HepG2	liver:	n/a	n/a
34	EGR1	chr3:179370057-179370925	HCT-116	colon:	n/a	chr3:179370276-179370290 chr3:179370274-179370284 chr3:179370687-179370701 chr3:179370257-179370271 chr3:179370729-179370742 chr3:179370730-179370740
35	ZBTB7A	chr3:179370280-179371779	ECC-1	luminal epithelium:	n/a	chr3:179370729-179370738
36	TEAD4	chr3:179370139-179371544	ECC-1	luminal epithelium:	n/a	n/a
37	RUNX3	chr3:179370164-179370875	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:179370170-179371655	GM12878	blood:	n/a	n/a
39	MAX	chr3:179370140-179371704	SK-N-SH	brain:	n/a	n/a
40	RCOR1	chr3:179370254-179370632	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr3:179370280-179370662	GM12892	blood:	n/a	n/a
42	POLR2A	chr3:179370400-179371509	ECC-1	luminal epithelium:	n/a	n/a
43	MAX	chr3:179370296-179371741	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:179370194-179371625	GM12892	blood:	n/a	n/a
45	MXI1	chr3:179369874-179371862	IMR90	lung:	n/a	n/a
46	POLR2A	chr3:179369989-179370867	SK-N-MC	brain:	n/a	n/a
47	ARID3A	chr3:179370296-179370931	HepG2	liver:	n/a	n/a
48	MYC	chr3:179370589-179370841	HepG2	liver:	n/a	n/a
49	POLR2A	chr3:179370112-179371775	GM19099	blood:	n/a	n/a
50	POLR2A	chr3:179370297-179371607	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:179062475..179065895-chr3:179368714..179370965,3	MCF-7	breast:
2	chr3:172467247..172468788-chr3:179370430..179372469,2	MCF-7	breast:
3	chr3:179279862..179282588-chr3:179370567..179372088,2	MCF-7	breast:
4	chr3:179369074..179371005-chr9:91932390..91934959,2	MCF-7	breast:

Variant related genes	Relation type
USP13	TF binding region
ENSG00000243977	TF binding region
ENSG00000187742	Chromatin interaction
ENSG00000114346	Chromatin interaction
ENSG00000136518	Chromatin interaction
ENSG00000171109	Chromatin interaction

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

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

rs_ID	r²[population]
rs28498062	1.00[EUR][1000 genomes]
rs6771683	1.00[AMR][1000 genomes]
rs6784464	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6805470	1.00[AMR][1000 genomes]
rs73058618	1.00[EUR][1000 genomes]
rs73058619	1.00[EUR][1000 genomes]
rs73058627	1.00[EUR][1000 genomes]
rs7616850	1.00[AMR][1000 genomes]
rs7618835	1.00[AMR][1000 genomes]
rs7619335	1.00[AMR][1000 genomes]
rs7625978	1.00[AMR][1000 genomes]
rs9811751	1.00[CEU][hapmap]
rs9832389	1.00[CEU][hapmap]
rs9847180	1.00[CEU][hapmap]
rs9850496	1.00[CEU][hapmap]
rs9872192	1.00[CEU][hapmap]
rs9881760	1.00[YRI][hapmap]

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	esv3400340	chr3:179369683-179372231	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	esv3450815	chr3:179370008-179372006	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 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	chr3:179369600-179372400	Active TSS	NHDF-Ad	bronchial
2	chr3:179369600-179372600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr3:179369800-179370600	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr3:179369800-179370600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:179369800-179371800	Active TSS	Brain Cingulate Gyrus	brain
6	chr3:179369800-179372000	Active TSS	Stomach Smooth Muscle	stomach
7	chr3:179369800-179372200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:179369800-179372200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:179369800-179372200	Active TSS	Fetal Brain Female	brain
10	chr3:179369800-179372400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr3:179369800-179372400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:179369800-179372400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:179369800-179372400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:179369800-179372400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:179369800-179372600	Active TSS	HSMMtube	muscle
16	chr3:179370000-179370600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr3:179370000-179370600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:179370000-179370600	Flanking Active TSS	Liver	Liver
19	chr3:179370000-179370600	Enhancers	Stomach Mucosa	stomach
20	chr3:179370000-179370600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
21	chr3:179370000-179370800	Active TSS	Right Atrium	heart
22	chr3:179370000-179371000	Active TSS	Primary B cells from cord blood	blood
23	chr3:179370000-179371000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:179370000-179371000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:179370000-179371400	Active TSS	Duodenum Mucosa	Duodenum
26	chr3:179370000-179371400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr3:179370000-179371600	Active TSS	Adipose Nuclei	Adipose
28	chr3:179370000-179371600	Active TSS	Fetal Muscle Trunk	muscle
29	chr3:179370000-179371800	Active TSS	Brain Substantia Nigra	brain
30	chr3:179370000-179371800	Active TSS	Gastric	stomach
31	chr3:179370000-179372000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:179370000-179372000	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr3:179370000-179372000	Active TSS	Primary T cells from cord blood	blood
34	chr3:179370000-179372000	Active TSS	Brain Angular Gyrus	brain
35	chr3:179370000-179372000	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr3:179370000-179372000	Active TSS	Fetal Lung	lung
37	chr3:179370000-179372000	Active TSS	Fetal Stomach	stomach
38	chr3:179370000-179372000	Active TSS	HMEC	breast
39	chr3:179370000-179372200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:179370000-179372200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr3:179370000-179372200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:179370000-179372200	Active TSS	Aorta	Aorta
43	chr3:179370000-179372200	Active TSS	Fetal Brain Male	brain
44	chr3:179370000-179372200	Active TSS	HSMM	muscle
45	chr3:179370000-179372600	Active TSS	H9 Cell Line	embryonic stem cell
46	chr3:179370000-179372600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:179370000-179372600	Active TSS	Fetal Kidney	kidney
48	chr3:179370000-179372600	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr3:179370000-179372800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:179370000-179372800	Active TSS	iPS-20b Cell Line	embryonic stem cell

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