Variant report

Variant	rs59158354
Chromosome Location	chr11:9532437-9532438
allele	G/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	STAT3	chr11:9532183-9532637	GM12878	blood:	n/a	n/a
2	NFIC	chr11:9532256-9532818	GM12878	blood:	n/a	n/a
3	BATF	chr11:9532429-9532620	GM12878	blood:	n/a	n/a
4	NFIC	chr11:9532287-9532884	GM12878	blood:	n/a	n/a
5	SP1	chr11:9532336-9532730	GM12878	blood:	n/a	n/a
6	JUND	chr11:9532335-9532611	HepG2	liver:	n/a	n/a
7	TCF12	chr11:9532037-9532828	A549	lung:	n/a	chr11:9532395-9532404
8	EBF1	chr11:9532433-9532839	GM12878	blood:	n/a	n/a
9	HDAC2	chr11:9532189-9532724	HepG2	liver:	n/a	chr11:9532395-9532404
10	NFIC	chr11:9532001-9532830	HepG2	liver:	n/a	n/a
11	MEF2A	chr11:9532249-9532780	GM12878	blood:	n/a	n/a
12	STAT1	chr11:9532419-9532535	GM12878	blood:	n/a	n/a
13	SP1	chr11:9532319-9532779	GM12878	blood:	n/a	n/a
14	ZBTB33	chr11:9532223-9532745	HepG2	liver:	n/a	n/a
15	MTA3	chr11:9532260-9532838	GM12878	blood:	n/a	n/a
16	RCOR1	chr11:9532373-9532737	GM12878	blood:	n/a	n/a
17	FOSL2	chr11:9532358-9532616	A549	lung:	n/a	n/a
18	FOSL2	chr11:9532035-9532715	A549	lung:	n/a	chr11:9532294-9532306
19	ARID3A	chr11:9532039-9532748	HepG2	liver:	n/a	n/a
20	EP300	chr11:9532055-9532741	HepG2	liver:	n/a	chr11:9532395-9532405
21	EBF1	chr11:9532265-9532820	GM12878	blood:	n/a	n/a
22	FOXA2	chr11:9532057-9532844	A549	lung:	n/a	n/a
23	TCF7L2	chr11:9532021-9532726	HepG2	liver:	n/a	n/a
24	ELF1	chr11:9532233-9532630	HepG2	liver:	n/a	n/a
25	CREB1	chr11:9532119-9532721	HepG2	liver:	n/a	n/a
26	FOXM1	chr11:9532276-9532801	GM12878	blood:	n/a	n/a
27	BCL11A	chr11:9532352-9532762	GM12878	blood:	n/a	chr11:9532613-9532622
28	EP300	chr11:9532104-9532651	A549	lung:	n/a	chr11:9532395-9532405
29	RUNX3	chr11:9532319-9532928	GM12878	blood:	n/a	chr11:9532595-9532604 chr11:9532595-9532604
30	POU2F2	chr11:9532344-9532801	GM12878	blood:	n/a	chr11:9532610-9532620 chr11:9532609-9532621 chr11:9532610-9532620 chr11:9532603-9532625
31	EP300	chr11:9532161-9532730	HepG2	liver:	n/a	chr11:9532395-9532405
32	BCL3	chr11:9532133-9532611	A549	lung:	n/a	n/a
33	PAX5	chr11:9532434-9532631	GM12878	blood:	n/a	n/a
34	NFIC	chr11:9532154-9532739	HepG2	liver:	n/a	n/a
35	EP300	chr11:9532225-9532654	HepG2	liver:	n/a	chr11:9532395-9532405
36	SP1	chr11:9532135-9532618	A549	lung:	n/a	n/a
37	MYBL2	chr11:9532102-9532776	HepG2	liver:	n/a	n/a
38	PBX3	chr11:9532429-9532635	GM12878	blood:	n/a	n/a
39	HDAC2	chr11:9532157-9532726	HepG2	liver:	n/a	chr11:9532395-9532404
40	CEBPB	chr11:9532175-9532996	HepG2	liver:	n/a	n/a
41	CREB1	chr11:9532253-9532665	GM12878	blood:	n/a	n/a
42	CUX1	chr11:9532256-9532725	GM12878	blood:	n/a	n/a
43	MXI1	chr11:9532167-9532656	HepG2	liver:	n/a	n/a
44	FOXA2	chr11:9532121-9532816	A549	lung:	n/a	n/a
45	EP300	chr11:9532356-9532763	GM12878	blood:	n/a	chr11:9532395-9532405
46	MXI1	chr11:9532232-9532706	GM12878	blood:	n/a	n/a
47	JUND	chr11:9532249-9532659	A549	lung:	n/a	chr11:9532294-9532306
48	REST	chr11:9532199-9532587	A549	lung:	n/a	n/a
49	RCOR1	chr11:9532183-9532656	HepG2	liver:	n/a	n/a
50	MAX	chr11:9532253-9532575	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9480637..9483121-chr11:9531195..9534021,2	MCF-7	breast:

Variant related genes	Relation type
ZNF143	TF binding region
ENSG00000166478	Chromatin interaction
ENSG00000268403	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11042379	0.83[AFR][1000 genomes]
rs12274646	0.83[AFR][1000 genomes]
rs34972213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56080598	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57050521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58602953	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59113683	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59571955	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60482254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404392	1.00[AMR][1000 genomes]
rs73406261	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406268	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406269	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406283	0.87[AFR][1000 genomes]
rs73406286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406301	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
3	nsv1039537	chr11:9455387-9535970	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9484600-9544800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:9491400-9551600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:9501800-9534000	Weak transcription	Psoas Muscle	Psoas
4	chr11:9518800-9534000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:9519200-9534200	Weak transcription	Fetal Brain Female	brain
6	chr11:9521000-9545200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:9523000-9534000	Weak transcription	HMEC	breast
8	chr11:9523400-9534000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:9523400-9534000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:9523400-9534000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:9523400-9534000	Weak transcription	Aorta	Aorta
12	chr11:9523400-9534000	Weak transcription	Brain Angular Gyrus	brain
13	chr11:9523400-9534000	Weak transcription	Fetal Brain Male	brain
14	chr11:9523400-9534200	Weak transcription	Right Ventricle	heart
15	chr11:9523400-9550800	Weak transcription	Colonic Mucosa	Colon
16	chr11:9523400-9551000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:9525200-9533600	Weak transcription	Placenta	Placenta
18	chr11:9525400-9534000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:9527000-9532600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr11:9528000-9534800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr11:9528000-9540000	Strong transcription	Fetal Thymus	thymus
22	chr11:9528400-9533600	Weak transcription	Fetal Lung	lung
23	chr11:9528600-9532600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:9528800-9532800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:9528800-9534000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:9528800-9534000	Weak transcription	Ovary	ovary
27	chr11:9528800-9534200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:9528800-9534200	Weak transcription	Hela-S3	cervix
29	chr11:9528800-9550400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr11:9529200-9550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr11:9529600-9534000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr11:9529800-9532800	Strong transcription	K562	blood
33	chr11:9530000-9534000	Enhancers	Fetal Intestine Large	intestine
34	chr11:9530000-9541000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:9530200-9532600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:9530200-9538400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:9530200-9538800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr11:9530200-9539600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:9530200-9540000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:9530200-9540200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr11:9530200-9541400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:9530200-9541400	Strong transcription	Adipose Nuclei	Adipose
43	chr11:9530200-9544600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:9530200-9551000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:9530400-9533600	Weak transcription	NHEK	skin
46	chr11:9530400-9539400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr11:9530600-9533600	Weak transcription	Colon Smooth Muscle	Colon
48	chr11:9530600-9534000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:9530600-9534000	Enhancers	HepG2	liver
50	chr11:9530800-9533600	Weak transcription	Placenta Amnion	Placenta Amnion

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