Variant report

Variant	rs11229028
Chromosome Location	chr11:57193918-57193919
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	POLR2A	chr11:57191261-57195084	K562	blood:	n/a	n/a
2	MAX	chr11:57192105-57195056	NB4	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
3	POLR2A	chr11:57191114-57195043	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:57191115-57195177	GM12892	blood:	n/a	n/a
5	STAT3	chr11:57193762-57194315	MCF10A-Er-Src	breast:	n/a	chr11:57193912-57193920
6	MAX	chr11:57191980-57195156	K562	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
7	MTA3	chr11:57191526-57195524	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:57191591-57194992	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:57193648-57194922	K562	blood:	n/a	n/a
10	POLR2A	chr11:57191113-57195429	HL-60	blood:	n/a	n/a
11	MYC	chr11:57193487-57194164	K562	blood:	n/a	chr11:57193991-57194004 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193993-57194003 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57193992-57194001 chr11:57193992-57194003 chr11:57193992-57194003
12	POLR2A	chr11:57192189-57195457	Raji	blood:	n/a	n/a
13	RCOR1	chr11:57192103-57194085	IMR90	lung:	n/a	n/a
14	POLR2A	chr11:57191441-57195068	GM18526	blood:	n/a	n/a
15	POLR2A	chr11:57192099-57194232	GM12878	blood:	n/a	n/a
16	CEBPB	chr11:57193902-57194214	K562	blood:	n/a	n/a
17	POLR2A	chr11:57193531-57194118	U87	brain:	n/a	n/a
18	MTA3	chr11:57191939-57194306	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:57193811-57194996	GM12878	blood:	n/a	n/a
20	MYC	chr11:57192097-57195095	NB4	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
21	STAT3	chr11:57193697-57194305	MCF10A-Er-Src	breast:	n/a	chr11:57193912-57193920 chr11:57193733-57193741 chr11:57193754-57193766
22	YY1	chr11:57193770-57194160	GM12892	blood:	n/a	n/a
23	MYC	chr11:57192128-57194621	K562	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
24	PML	chr11:57191892-57195093	GM12878	blood:	n/a	chr11:57192441-57192450
25	USF1	chr11:57193789-57194240	H1-hESC	embryonic stem cell:	n/a	n/a
26	TBP	chr11:57193796-57194979	GM12878	blood:	n/a	n/a
27	USF1	chr11:57193838-57194180	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr11:57191153-57195123	GM12891	blood:	n/a	n/a
29	POLR2A	chr11:57192095-57194977	NB4	blood:	n/a	n/a
30	USF1	chr11:57193824-57194118	K562	blood:	n/a	n/a
31	NR2F2	chr11:57193165-57194182	K562	blood:	n/a	n/a
32	POLR2A	chr11:57191285-57195328	K562	blood:	n/a	n/a
33	MAX	chr11:57193717-57195177	HCT-116	colon:	n/a	chr11:57193991-57194004 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193993-57194003 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57193992-57194001 chr11:57193992-57194003 chr11:57193992-57194003
34	POLR2A	chr11:57192131-57195018	GM15510	blood:	n/a	n/a
35	RUNX3	chr11:57192047-57195167	GM12878	blood:	n/a	n/a
36	POLR2A	chr11:57191219-57194857	GM12891	blood:	n/a	n/a
37	MYC	chr11:57192188-57195515	MCF10A-Er-Src	breast:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
38	MAX	chr11:57193464-57194850	H1-hESC	embryonic stem cell:	n/a	chr11:57193991-57194004 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193993-57194003 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57193992-57194001 chr11:57193992-57194003 chr11:57193992-57194003
39	MAX	chr11:57193821-57194566	H1-hESC	embryonic stem cell:	n/a	chr11:57193991-57194004 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193993-57194003 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57193992-57194001 chr11:57193992-57194003 chr11:57193992-57194003
40	POLR2A	chr11:57192079-57195002	GM12878	blood:	n/a	n/a
41	YY1	chr11:57193842-57194143	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr11:57191305-57194984	GM12878	blood:	n/a	n/a
43	YY1	chr11:57193772-57194144	K562	blood:	n/a	n/a
44	WRNIP1	chr11:57191369-57195127	GM12878	blood:	n/a	n/a
45	POLR2A	chr11:57191179-57195028	K562	blood:	n/a	n/a
46	POLR2A	chr11:57191196-57195715	U87	brain:	n/a	n/a
47	POLR2A	chr11:57191294-57195046	GM12892	blood:	n/a	n/a
48	POLR2A	chr11:57193524-57194315	GM12891	blood:	n/a	n/a
49	E2F6	chr11:57192150-57195054	K562	blood:	n/a	chr11:57192552-57192561 chr11:57194364-57194373 chr11:57193865-57193872 chr11:57193865-57193872 chr11:57193865-57193872
50	USF2	chr11:57192132-57194876	GM12878	blood:	n/a	chr11:57192756-57192765 chr11:57192756-57192765 chr11:57194437-57194453 chr11:57192875-57192891 chr11:57192755-57192766

No.	Distal block	Cell Line	Cell type
1	chr11:57092537..57094239-chr11:57192344..57194712,2	K562	blood:
2	chr11:57191864..57194047-chr11:57412922..57415205,2	K562	blood:
3	chr11:57190585..57194081-chr11:57295965..57298665,6	K562	blood:
4	chr11:57192480..57194732-chr11:57434843..57437661,2	K562	blood:
5	chr11:57094351..57096693-chr11:57193203..57197242,3	K562	blood:

Variant related genes	Relation type
ENSG00000254979	TF binding region
SLC43A3	TF binding region
ENSG00000166793	Chromatin interaction
ENSG00000156599	Chromatin interaction
ENSG00000254602	Chromatin interaction
ENSG00000134809	Chromatin interaction
ENSG00000238692	Chromatin interaction
ENSG00000254662	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11820985	0.96[ASN][1000 genomes]
rs11822095	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11822910	0.98[ASN][1000 genomes]
rs11827928	0.98[ASN][1000 genomes]
rs11828218	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422015	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12788236	0.81[ASN][1000 genomes]
rs2250887	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2439448	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581924	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2581927	0.81[EUR][1000 genomes]
rs2581928	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2584857	1.00[YRI][hapmap]
rs2584858	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2729389	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2729392	0.81[EUR][1000 genomes]
rs4477456	0.98[ASN][1000 genomes]
rs4529894	0.98[ASN][1000 genomes]
rs60961847	0.91[ASN][1000 genomes]
rs61886978	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7106223	0.91[ASN][1000 genomes]
rs7122734	0.93[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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11229028	TIMM10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57186000-57194000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:57189800-57194000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
3	chr11:57191200-57194000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr11:57191200-57194400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr11:57191400-57194000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
6	chr11:57191400-57194000	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr11:57191400-57194200	Transcr. at gene 5' and 3'	K562	blood
8	chr11:57191600-57194000	Enhancers	Ovary	ovary
9	chr11:57191600-57194200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:57191600-57195200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:57191600-57195600	Enhancers	Spleen	Spleen
12	chr11:57191800-57194000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:57191800-57194000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr11:57191800-57194200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:57191800-57194200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:57191800-57194200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr11:57191800-57194200	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr11:57191800-57194800	Enhancers	Fetal Heart	heart
19	chr11:57191800-57195000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:57191800-57195000	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr11:57191800-57195000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr11:57191800-57195200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr11:57192000-57194000	Enhancers	Lung	lung
24	chr11:57192000-57194000	Enhancers	HSMMtube	muscle
25	chr11:57192000-57194200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr11:57192000-57194200	Flanking Active TSS	Liver	Liver
27	chr11:57192000-57194400	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr11:57192000-57194600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr11:57192000-57195000	Flanking Active TSS	Fetal Thymus	thymus
30	chr11:57192200-57194000	Enhancers	Primary B cells from peripheral blood	blood
31	chr11:57192200-57194200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr11:57192200-57194200	Enhancers	Brain Substantia Nigra	brain
33	chr11:57192200-57195000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr11:57192200-57195000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr11:57192200-57195200	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr11:57192200-57195400	Flanking Active TSS	Osteobl	bone
37	chr11:57192400-57194000	Genic enhancers	Fetal Intestine Small	intestine
38	chr11:57192400-57195400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr11:57192600-57194000	Flanking Active TSS	Esophagus	oesophagus
40	chr11:57192800-57194000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:57192800-57194000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr11:57192800-57194000	Enhancers	NH-A	brain
43	chr11:57192800-57194200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr11:57192800-57194200	Enhancers	Stomach Mucosa	stomach
45	chr11:57192800-57194400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:57192800-57194400	Flanking Active TSS	HSMM	muscle
47	chr11:57192800-57194800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:57192800-57195000	Flanking Active TSS	NHDF-Ad	bronchial
49	chr11:57192800-57195200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:57193000-57194400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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