Variant report

Variant	rs470941
Chromosome Location	chr11:119999755-119999756
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	CEBPB	chr11:119999514-119999823	IMR90	lung:	n/a	n/a
2	EP300	chr11:119999656-119999756	HepG2	liver:	n/a	n/a
3	IRF3	chr11:119999324-120000060	Hela-S3	cervix:	n/a	chr11:119999563-119999573 chr11:119999562-119999571 chr11:119999559-119999573
4	MYC	chr11:119999448-120000027	MCF10A-Er-Src	breast:	n/a	n/a
5	NR3C1	chr11:119999547-119999767	A549	lung:	n/a	n/a
6	CEBPB	chr11:119999481-119999865	A549	lung:	n/a	n/a
7	CEBPB	chr11:119999416-119999869	A549	lung:	n/a	n/a
8	RCOR1	chr11:119999253-120000037	Hela-S3	cervix:	n/a	n/a
9	MAX	chr11:119999404-119999883	Hela-S3	cervix:	n/a	n/a
10	CREB1	chr11:119999488-119999820	A549	lung:	n/a	n/a
11	CEBPB	chr11:119999362-120000101	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr11:119999294-119999934	Hela-S3	cervix:	n/a	n/a
13	FOS	chr11:119999211-119999962	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr11:119999499-119999895	Hela-S3	cervix:	n/a	chr11:119999736-119999747 chr11:119999738-119999746 chr11:119999567-119999579
15	CEBPB	chr11:119999481-119999836	A549	lung:	n/a	n/a
16	ELK1	chr11:119999364-119999767	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr11:119999467-120000161	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr11:119999447-119999937	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr11:119999505-120000050	MCF10A-Er-Src	breast:	n/a	chr11:119999736-119999747 chr11:119999738-119999746 chr11:119999567-119999579
20	MAX	chr11:119999355-120000050	Hela-S3	cervix:	n/a	n/a
21	NR3C1	chr11:119999434-119999798	A549	lung:	n/a	n/a
22	POLR2A	chr11:119999280-119999935	Hela-S3	cervix:	n/a	n/a
23	USF2	chr11:119999324-120000057	Hela-S3	cervix:	n/a	n/a
24	CEBPB	chr11:119999480-119999858	HepG2	liver:	n/a	n/a
25	STAT3	chr11:119999428-120000736	MCF10A-Er-Src	breast:	n/a	chr11:120000440-120000449 chr11:119999736-119999747 chr11:119999738-119999746 chr11:119999567-119999579 chr11:120000440-120000463 chr11:120000438-120000449 chr11:120000439-120000448
26	FOXA1	chr11:119999178-119999877	T-47D	breast:	n/a	n/a
27	MYC	chr11:119999464-119999879	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr11:119999571-119999781	K562	blood:	n/a	n/a
29	TBP	chr11:119999298-119999977	Hela-S3	cervix:	n/a	n/a
30	GATA3	chr11:119999469-119999829	T-47D	breast:	n/a	chr11:119999482-119999499
31	BRCA1	chr11:119999519-119999869	Hela-S3	cervix:	n/a	n/a
32	GATA3	chr11:119998961-119999861	T-47D	breast:	n/a	chr11:119999482-119999499
33	MYC	chr11:119999448-120000494	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr11:119999495-119999974	MCF10A-Er-Src	breast:	n/a	n/a
35	MAFK	chr11:119999530-120000045	Hela-S3	cervix:	n/a	n/a
36	MAZ	chr11:119999433-119999861	Hela-S3	cervix:	n/a	n/a
37	STAT1	chr11:119999327-120000709	Hela-S3	cervix:	n/a	chr11:120000440-120000449 chr11:119999736-119999747 chr11:119999738-119999746 chr11:119999567-119999579 chr11:120000440-120000463 chr11:120000439-120000448
38	FOS	chr11:119999528-119999854	MCF10A-Er-Src	breast:	n/a	n/a
39	CEBPB	chr11:119999490-119999893	ECC-1	luminal epithelium:	n/a	n/a
40	CEBPB	chr11:119999515-119999889	ECC-1	luminal epithelium:	n/a	n/a
41	EP300	chr11:119999415-119999934	T-47D	breast:	n/a	n/a
42	RFX5	chr11:119999412-119999865	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr11:119999200-120000342	Hela-S3	cervix:	n/a	n/a
44	EP300	chr11:119999356-119999886	T-47D	breast:	n/a	n/a
45	POLR2A	chr11:119999072-120000644	MCF10A-Er-Src	breast:	n/a	n/a
46	GTF2F1	chr11:119999347-120000079	Hela-S3	cervix:	n/a	n/a
47	TFAP2A	chr11:119999418-119999997	Hela-S3	cervix:	n/a	n/a
48	E2F4	chr11:119999526-119999870	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr11:119999429-119999827	Hela-S3	cervix:	n/a	n/a
50	TCF7L2	chr11:119999441-119999904	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:119992602..119994710-chr11:119998240..120000665,2	MCF-7	breast:
2	chr11:119993537..119997499-chr11:119998076..120003019,6	K562	blood:
3	chr11:119999095..120001127-chr11:120038214..120040210,2	MCF-7	breast:
4	chr11:119995303..119997544-chr11:119999140..120002182,3	MCF-7	breast:

Variant related genes	Relation type
TRIM29	TF binding region
ENSG00000137699	Chromatin interaction
ENSG00000176984	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1790476	0.85[EUR][1000 genomes]
rs2444240	0.87[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs470370	0.81[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs470373	0.84[ASN][1000 genomes]
rs470392	0.86[CHB][hapmap]
rs470411	0.81[CEU][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs470645	0.88[JPT][hapmap]
rs470725	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs470876	0.81[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs471001	0.83[ASN][1000 genomes]
rs488672	0.87[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs531260	0.81[EUR][1000 genomes]
rs533636	0.87[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs550164	0.94[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs561498	0.90[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs566935	0.82[JPT][hapmap]
rs590843	0.86[CHB][hapmap]
rs605374	0.87[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs670855	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1050132	chr11:119976310-120010437	Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs470941	VPS11	cis	cerebellum	SCAN
rs470941	ABCG4	cis	cerebellum	SCAN
rs470941	THY1	cis	cerebellum	SCAN
rs470941	SORL1	cis	cerebellum	SCAN
rs470941	TRIM29	cis	Artery Tibial	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119993400-119999800	Weak transcription	Fetal Thymus	thymus
2	chr11:119993400-120000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:119993800-120001800	Weak transcription	Pancreas	Pancrea
4	chr11:119995200-120000200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:119997600-120003200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
6	chr11:119998000-120000200	Genic enhancers	Esophagus	oesophagus
7	chr11:119998600-120000400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr11:119998600-120000800	Enhancers	Rectal Smooth Muscle	rectum
9	chr11:119998600-120001200	Enhancers	Colon Smooth Muscle	Colon
10	chr11:119998800-119999800	Enhancers	Colonic Mucosa	Colon
11	chr11:119998800-120000200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:119998800-120000200	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr11:119998800-120000400	Enhancers	Duodenum Mucosa	Duodenum
14	chr11:119998800-120000400	Enhancers	Stomach Mucosa	stomach
15	chr11:119998800-120000600	Enhancers	Fetal Intestine Large	intestine
16	chr11:119998800-120000800	Enhancers	Fetal Intestine Small	intestine
17	chr11:119999000-119999800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:119999000-120000000	Enhancers	Adipose Nuclei	Adipose
19	chr11:119999000-120000600	Transcr. at gene 5' and 3'	NHEK	skin
20	chr11:119999000-120001400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:119999000-120001600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:119999000-120006400	Enhancers	Placenta	Placenta
23	chr11:119999200-119999800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:119999200-120000000	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr11:119999400-120000400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr11:119999600-119999800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:119999600-119999800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:119999600-119999800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:119999600-119999800	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr11:119999600-119999800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
31	chr11:119999600-119999800	Enhancers	Hela-S3	cervix
32	chr11:119999600-119999800	Enhancers	HMEC	breast
33	chr11:119999600-120000000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:119999600-120000000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle

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