Variant report

Variant	rs9870933
Chromosome Location	chr3:112372317-112372318
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	SP1	chr3:112371695-112373412	A549	lung:	n/a	chr3:112372883-112372904 chr3:112373077-112373091
2	ETS1	chr3:112371909-112372837	A549	lung:	n/a	n/a
3	EP300	chr3:112371809-112373383	A549	lung:	n/a	chr3:112372992-112373008 chr3:112372423-112372437 chr3:112373304-112373313 chr3:112373164-112373178
4	GATA3	chr3:112372196-112373027	MCF-7	breast:	n/a	chr3:112372931-112372939
5	RXRA	chr3:112372238-112373385	SK-N-SH	brain:	n/a	n/a
6	CEBPB	chr3:112372117-112372655	A549	lung:	n/a	n/a
7	ATF3	chr3:112371972-112373297	A549	lung:	n/a	n/a
8	EP300	chr3:112372106-112373929	SK-N-SH	brain:	n/a	chr3:112372992-112373008 chr3:112372423-112372437 chr3:112373304-112373313 chr3:112373164-112373178
9	BCL3	chr3:112371923-112373296	A549	lung:	n/a	n/a
10	TCF12	chr3:112372133-112374204	SK-N-SH	brain:	n/a	n/a
11	USF1	chr3:112372091-112372721	A549	lung:	n/a	n/a
12	JUND	chr3:112372239-112373952	SK-N-SH	brain:	n/a	chr3:112372365-112372374
13	FOSL2	chr3:112371751-112373413	A549	lung:	n/a	chr3:112372365-112372374
14	EP300	chr3:112372104-112373481	SK-N-SH	brain:	n/a	chr3:112372992-112373008 chr3:112372423-112372437 chr3:112373304-112373313 chr3:112373164-112373178
15	ZBTB33	chr3:112372304-112373269	SK-N-SH	brain:	n/a	n/a
16	MAX	chr3:112371779-112373349	A549	lung:	n/a	n/a
17	TCF12	chr3:112371646-112373440	A549	lung:	n/a	n/a
18	REST	chr3:112371911-112373274	A549	lung:	n/a	chr3:112373001-112373019 chr3:112373006-112373026
19	MYC	chr3:112372236-112372697	MCF10A-Er-Src	breast:	n/a	n/a
20	TEAD4	chr3:112372178-112373284	SK-N-SH	brain:	n/a	n/a
21	JUND	chr3:112372205-112373728	SK-N-SH	brain:	n/a	chr3:112372365-112372374
22	POLR2A	chr3:112372081-112373383	U87	brain:	n/a	n/a
23	TCF12	chr3:112372119-112373418	SK-N-SH	brain:	n/a	n/a
24	PBX3	chr3:112371989-112373315	A549	lung:	n/a	chr3:112372893-112372902
25	POLR2A	chr3:112372278-112373282	SK-N-SH	brain:	n/a	n/a
26	SP1	chr3:112371764-112373387	A549	lung:	n/a	chr3:112372883-112372904 chr3:112373077-112373091
27	MAZ	chr3:112371602-112373415	IMR90	lung:	n/a	n/a
28	NFIC	chr3:112372137-112373467	SK-N-SH	brain:	n/a	n/a
29	RAD21	chr3:112371842-112373469	A549	lung:	n/a	n/a
30	GABPA	chr3:112372187-112372782	A549	lung:	n/a	n/a
31	FOXA2	chr3:112371982-112372759	A549	lung:	n/a	n/a
32	NR3C1	chr3:112372094-112373163	A549	lung:	n/a	chr3:112372970-112372984 chr3:112372679-112372705 chr3:112372966-112372987 chr3:112372964-112372990 chr3:112372679-112372705 chr3:112372964-112372990
33	FOSL2	chr3:112372010-112373283	A549	lung:	n/a	chr3:112372365-112372374
34	SIX5	chr3:112372302-112372743	A549	lung:	n/a	n/a
35	GATA3	chr3:112372005-112373875	SK-N-SH	brain:	n/a	chr3:112372931-112372939
36	TBP	chr3:112372286-112372348	Hela-S3	cervix:	n/a	n/a
37	FOS	chr3:112372275-112373306	MCF10A-Er-Src	breast:	n/a	chr3:112372365-112372374
38	NR3C1	chr3:112372013-112373138	A549	lung:	n/a	chr3:112372970-112372984 chr3:112372679-112372705 chr3:112372966-112372987 chr3:112372964-112372990 chr3:112372679-112372705 chr3:112372964-112372990
39	ATF3	chr3:112371968-112373312	A549	lung:	n/a	n/a
40	TCF12	chr3:112371927-112373261	A549	lung:	n/a	n/a
41	FOXA2	chr3:112371988-112373252	A549	lung:	n/a	n/a
42	CEBPB	chr3:112372036-112372785	A549	lung:	n/a	n/a
43	CEBPB	chr3:112372133-112373253	IMR90	lung:	n/a	chr3:112372894-112372902
44	GABPA	chr3:112372220-112373237	A549	lung:	n/a	n/a
45	TEAD4	chr3:112372122-112373475	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr3:112372087-112373315	U87	brain:	n/a	n/a
47	RAD21	chr3:112372196-112373385	A549	lung:	n/a	n/a
48	MAFK	chr3:112372182-112373248	IMR90	lung:	n/a	n/a
49	E2F6	chr3:112372029-112373369	A549	lung:	n/a	chr3:112372894-112372903
50	ZBTB33	chr3:112372232-112373070	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:112358658..112361314-chr3:112370699..112373290,3	MCF-7	breast:
2	chr3:112363786..112368966-chr3:112369502..112375118,11	MCF-7	breast:
3	chr3:112362097..112368318-chr3:112369170..112375638,8	MCF-7	breast:

Variant related genes	Relation type
CCDC80	TF binding region
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs3842905	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes]
rs56302621	0.80[AMR][1000 genomes]
rs6438086	0.91[TSI][hapmap]
rs6438087	0.89[TSI][hapmap]
rs6768072	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6772337	0.81[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611898	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7620601	0.85[TSI][hapmap]
rs7630314	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9815819	0.89[TSI][hapmap]
rs9845240	0.81[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9870933	ESAM	trans	parietal	SCAN
rs9870933	BOC	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112363400-112373600	Weak transcription	Esophagus	oesophagus
2	chr3:112364600-112372800	Enhancers	Osteobl	bone
3	chr3:112366400-112372400	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:112366400-112372600	Enhancers	NHDF-Ad	bronchial
5	chr3:112366400-112373800	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:112367000-112373800	Enhancers	HSMM	muscle
7	chr3:112367800-112372800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:112368000-112372800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:112368000-112375000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:112368200-112372600	Enhancers	HSMMtube	muscle
11	chr3:112368200-112372800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:112368200-112375200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:112368600-112373600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:112370800-112372800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:112371400-112372400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:112371400-112375200	Enhancers	HMEC	breast
17	chr3:112371600-112374000	Flanking Active TSS	A549	lung
18	chr3:112371800-112372400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr3:112371800-112372800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:112371800-112373000	Enhancers	Adipose Nuclei	Adipose
21	chr3:112371800-112373400	Enhancers	NHLF	lung
22	chr3:112371800-112373600	Enhancers	NH-A	brain
23	chr3:112371800-112374000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:112371800-112374000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:112371800-112374000	Enhancers	Placenta	Placenta
26	chr3:112371800-112375000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:112372000-112372400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr3:112372000-112375000	Enhancers	Fetal Lung	lung
29	chr3:112372200-112372400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:112372200-112372800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:112372200-112373200	Flanking Active TSS	NHEK	skin
32	chr3:112372200-112373400	Weak transcription	Placenta Amnion	Placenta Amnion

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