Variant report

Variant	rs11172823
Chromosome Location	chr12:59312113-59312114
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	MYC	chr12:59311692-59312476	MCF10A-Er-Src	breast:	n/a	chr12:59311729-59311738 chr12:59311818-59311833 chr12:59311821-59311831 chr12:59311730-59311737 chr12:59311820-59311835
2	MYC	chr12:59310623-59312620	MCF10A-Er-Src	breast:	n/a	chr12:59311729-59311738 chr12:59311818-59311833 chr12:59311821-59311831 chr12:59311730-59311737 chr12:59311820-59311835
3	TCF7L2	chr12:59311592-59312714	HEK293	kidney:	n/a	n/a
4	POLR2A	chr12:59309378-59314838	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:59311533-59312305	PFSK-1	brain:	n/a	n/a
6	TAF1	chr12:59311749-59312199	PFSK-1	brain:	n/a	n/a
7	KAP1	chr12:59310275-59312520	HEK293	kidney:	n/a	n/a
8	KAP1	chr12:59310757-59312442	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59306615..59312160-chr12:59312563..59315284,9	MCF-7	breast:

Variant related genes	Relation type
LRIG3	TF binding region
ENSG00000257443	TF binding region
ENSG00000139263	Chromatin interaction
ENSG00000257443	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10877188	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10877198	0.80[EUR][1000 genomes]
rs11172824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172827	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11172831	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11172833	0.92[EUR][1000 genomes]
rs11172837	0.82[EUR][1000 genomes]
rs11172839	0.82[EUR][1000 genomes]
rs11172840	0.82[EUR][1000 genomes]
rs11172846	0.82[EUR][1000 genomes]
rs11172857	0.82[EUR][1000 genomes]
rs11172858	0.80[EUR][1000 genomes]
rs11172860	0.80[EUR][1000 genomes]
rs11172861	0.80[EUR][1000 genomes]
rs11172862	0.80[EUR][1000 genomes]
rs12368752	0.82[EUR][1000 genomes]
rs12370522	0.81[AMR][1000 genomes]
rs12423502	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12424788	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12426212	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12426555	0.85[CHB][hapmap];0.85[MEX][hapmap]
rs12426969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60522760	0.82[EUR][1000 genomes]
rs60984323	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61754220	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919461	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61919462	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61919464	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61919465	0.92[EUR][1000 genomes]
rs61919466	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61919469	0.82[EUR][1000 genomes]
rs61919471	0.80[EUR][1000 genomes]
rs61919513	0.82[EUR][1000 genomes]
rs61919518	0.82[EUR][1000 genomes]
rs61919519	0.82[EUR][1000 genomes]
rs61919520	0.80[EUR][1000 genomes]
rs61919521	0.82[EUR][1000 genomes]
rs61919523	0.82[EUR][1000 genomes]
rs61919524	0.80[EUR][1000 genomes]
rs61919525	0.80[EUR][1000 genomes]
rs6581224	0.80[EUR][1000 genomes]
rs7136193	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7138401	0.82[EUR][1000 genomes]
rs7294684	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7297094	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7301299	0.82[EUR][1000 genomes]
rs7302365	0.82[EUR][1000 genomes]
rs7303773	0.80[EUR][1000 genomes]
rs7309872	0.82[EUR][1000 genomes]
rs7963207	0.82[EUR][1000 genomes]
rs7968111	0.80[EUR][1000 genomes]
rs7969722	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7970054	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7980136	0.92[EUR][1000 genomes]
rs7980483	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9645802	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11172823	ESPL1	cis	cerebellum	SCAN
rs11172823	PIP4K2C	cis	cerebellum	SCAN
rs11172823	INHBE	cis	parietal	SCAN
rs11172823	INHBC	cis	parietal	SCAN
rs11172823	RAB5B	cis	cerebellum	SCAN
rs11172823	MBD6	cis	cerebellum	SCAN
rs11172823	COQ10A	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59302000-59313000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:59303200-59313400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:59303800-59312400	Weak transcription	Gastric	stomach
4	chr12:59303800-59313000	Weak transcription	Lung	lung
5	chr12:59304800-59312800	Weak transcription	Placenta	Placenta
6	chr12:59306600-59313000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:59308600-59314600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:59308800-59314600	Active TSS	Stomach Smooth Muscle	stomach
9	chr12:59309000-59312200	Flanking Active TSS	Osteobl	bone
10	chr12:59309000-59314400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr12:59309000-59314600	Active TSS	HMEC	breast
12	chr12:59309200-59312200	Enhancers	Fetal Heart	heart
13	chr12:59309200-59314600	Active TSS	Duodenum Mucosa	Duodenum
14	chr12:59309200-59314600	Active TSS	Fetal Intestine Small	intestine
15	chr12:59309200-59314600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr12:59309200-59314800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:59309200-59314800	Active TSS	Ovary	ovary
18	chr12:59309200-59315200	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr12:59309400-59315000	Active TSS	Fetal Muscle Trunk	muscle
20	chr12:59309800-59312400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:59309800-59313000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:59309800-59313000	Weak transcription	Esophagus	oesophagus
23	chr12:59309800-59313400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:59309800-59314600	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr12:59310000-59313400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:59310000-59315000	Active TSS	Fetal Intestine Large	intestine
27	chr12:59310000-59315200	Active TSS	Rectal Smooth Muscle	rectum
28	chr12:59310400-59312800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:59310400-59313000	Active TSS	Thymus	Thymus
30	chr12:59310400-59314400	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr12:59310400-59314800	Active TSS	Psoas Muscle	Psoas
32	chr12:59310400-59315200	Active TSS	Stomach Mucosa	stomach
33	chr12:59310600-59313600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:59310600-59314600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:59310600-59314600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:59310600-59314600	Active TSS	Fetal Stomach	stomach
37	chr12:59310600-59314600	Active TSS	NHLF	lung
38	chr12:59310600-59314800	Active TSS	Right Atrium	heart
39	chr12:59310600-59315000	Active TSS	Fetal Kidney	kidney
40	chr12:59310800-59312200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr12:59310800-59312200	Enhancers	Hela-S3	cervix
42	chr12:59310800-59312600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr12:59310800-59312600	Flanking Active TSS	HepG2	liver
44	chr12:59310800-59314600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:59310800-59314600	Active TSS	NHEK	skin
46	chr12:59310800-59314800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:59310800-59314800	Active TSS	Aorta	Aorta
48	chr12:59310800-59315000	Active TSS	Pancreas	Pancrea
49	chr12:59311000-59313400	Active TSS	Fetal Muscle Leg	muscle
50	chr12:59311000-59314400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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