Variant report

Variant	rs7102217
Chromosome Location	chr11:120187433-120187434
allele	C/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	MAX	chr11:120187352-120188026	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr11:120187380-120187995	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr11:120187333-120187901	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr11:120187302-120188135	HCT-116	colon:	n/a	n/a
5	MAX	chr11:120187287-120187926	MCF-7	breast:	n/a	n/a
6	NFIC	chr11:120187348-120188039	ECC-1	luminal epithelium:	n/a	chr11:120187655-120187671
7	POLR2A	chr11:120187423-120187933	HCT-116	colon:	n/a	n/a
8	SP1	chr11:120187273-120188383	HCT-116	colon:	n/a	chr11:120187804-120187814 chr11:120187804-120187814
9	CEBPB	chr11:120187331-120188073	HCT-116	colon:	n/a	chr11:120187672-120187683
10	SIN3AK20	chr11:120187323-120188223	MCF-7	breast:	n/a	n/a
11	GATA3	chr11:120187399-120187979	MCF-7	breast:	n/a	n/a
12	CEBPB	chr11:120187379-120188000	MCF-7	breast:	n/a	chr11:120187672-120187683
13	NFIC	chr11:120187332-120188074	ECC-1	luminal epithelium:	n/a	chr11:120187655-120187671
14	TCF12	chr11:120187353-120188106	ECC-1	luminal epithelium:	n/a	chr11:120187500-120187507 chr11:120187496-120187506
15	MAX	chr11:120187284-120188060	HCT-116	colon:	n/a	n/a
16	MAX	chr11:120187391-120188245	MCF-7	breast:	n/a	n/a
17	POLR2A	chr11:120187316-120187597	MCF-7	breast:	n/a	n/a
18	TCF12	chr11:120187376-120187951	ECC-1	luminal epithelium:	n/a	chr11:120187500-120187507 chr11:120187496-120187506
19	SP1	chr11:120187321-120188238	HCT-116	colon:	n/a	chr11:120187804-120187814 chr11:120187804-120187814
20	GATA3	chr11:120187433-120187870	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:120186835..120191514-chr11:120193209..120197461,6	MCF-7	breast:
2	chr11:120178572..120180297-chr11:120186032..120187655,2	K562	blood:
3	chr11:120106132..120109259-chr11:120185529..120190071,6	K562	blood:
4	chr11:120179013..120183815-chr11:120184501..120187839,4	MCF-7	breast:
5	chr11:120175506..120178899-chr11:120185723..120187781,3	MCF-7	breast:
6	chr11:120173473..120178843-chr11:120183667..120189130,9	MCF-7	breast:

Variant related genes	Relation type
POU2F3	TF binding region
ENSG00000137709	Chromatin interaction
ENSG00000181264	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10790376	0.89[EUR][1000 genomes]
rs10892561	0.84[EUR][1000 genomes]
rs11217816	0.87[CEU][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs35238955	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4938795	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7122401	0.91[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.90[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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7102217	ARHGEF12	cis	brain	BrainEAC
rs7102217	MPZL3	cis	parietal	SCAN
rs7102217	UPK2	cis	cerebellum	SCAN
rs7102217	ZNF259	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120177200-120187600	Weak transcription	Gastric	stomach
2	chr11:120178200-120187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:120183800-120187600	Weak transcription	Small Intestine	intestine
4	chr11:120185400-120187800	Enhancers	Placenta	Placenta
5	chr11:120185400-120189000	Enhancers	Fetal Heart	heart
6	chr11:120185600-120188000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:120185800-120187800	Enhancers	Esophagus	oesophagus
8	chr11:120186000-120187600	Weak transcription	Lung	lung
9	chr11:120186800-120188800	Enhancers	Right Atrium	heart
10	chr11:120187000-120187800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:120187000-120187800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr11:120187000-120188000	Enhancers	Fetal Muscle Leg	muscle
13	chr11:120187000-120188400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr11:120187000-120188400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:120187000-120188400	Enhancers	Fetal Lung	lung
16	chr11:120187000-120188400	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr11:120187000-120188600	Enhancers	Ovary	ovary
18	chr11:120187000-120188600	Enhancers	Stomach Mucosa	stomach
19	chr11:120187000-120188600	Enhancers	HMEC	breast
20	chr11:120187200-120187600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr11:120187200-120187600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:120187200-120187600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:120187200-120187600	Enhancers	Rectal Smooth Muscle	rectum
24	chr11:120187200-120187600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
25	chr11:120187200-120187600	Enhancers	Stomach Smooth Muscle	stomach
26	chr11:120187200-120187800	Enhancers	Right Ventricle	heart
27	chr11:120187200-120188000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:120187200-120188000	Enhancers	Fetal Muscle Trunk	muscle
29	chr11:120187200-120188200	Enhancers	Aorta	Aorta
30	chr11:120187200-120188200	Enhancers	Pancreas	Pancrea
31	chr11:120187200-120188400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:120187200-120188400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:120187200-120188400	Enhancers	Fetal Stomach	stomach
34	chr11:120187200-120188400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr11:120187200-120188600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr11:120187200-120188800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:120187200-120188800	Enhancers	Colonic Mucosa	Colon
38	chr11:120187200-120188800	Enhancers	Left Ventricle	heart
39	chr11:120187200-120189600	Enhancers	Fetal Intestine Small	intestine
40	chr11:120187200-120189800	Enhancers	Fetal Intestine Large	intestine
41	chr11:120187400-120187600	Enhancers	H9 Cell Line	embryonic stem cell
42	chr11:120187400-120187600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr11:120187400-120187600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
44	chr11:120187400-120187800	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr11:120187400-120187800	Bivalent Enhancer	NHLF	lung
46	chr11:120187400-120188000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:120187400-120188200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:120187400-120188200	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr11:120187400-120188200	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr11:120187400-120188200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell

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