Variant report

Variant	rs2291841
Chromosome Location	chr11:5710896-5710897
allele	A/C
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	SIN3A	chr11:5710815-5711472	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:5710646-5712030	GM12892	blood:	n/a	n/a
3	FOS	chr11:5710726-5711025	MCF10A-Er-Src	breast:	n/a	chr11:5710859-5710869 chr11:5710859-5710869
4	POLR2A	chr11:5710722-5712585	GM18951	blood:	n/a	n/a
5	EP300	chr11:5710546-5711204	GM12878	blood:	n/a	n/a
6	TAF1	chr11:5710827-5711847	H1-hESC	embryonic stem cell:	n/a	n/a
7	EBF1	chr11:5710706-5711164	GM12878	blood:	n/a	chr11:5710914-5710924
8	CEBPB	chr11:5710576-5712088	GM12878	blood:	n/a	chr11:5711132-5711145
9	POLR2A	chr11:5710194-5714647	GM12891	blood:	n/a	n/a
10	POLR2A	chr11:5710610-5712552	GM19099	blood:	n/a	n/a
11	ELF1	chr11:5710760-5711193	GM12878	blood:	n/a	n/a
12	CEBPB	chr11:5710867-5711240	H1-hESC	embryonic stem cell:	n/a	chr11:5711132-5711145
13	POLR2A	chr11:5710770-5711161	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr11:5710757-5711219	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr11:5710791-5712498	GM12878	blood:	n/a	n/a
16	IRF1	chr11:5710830-5711060	K562	blood:	n/a	chr11:5710983-5710996 chr11:5710964-5710974 chr11:5710960-5710974 chr11:5710978-5710991 chr11:5710982-5710996
17	POLR2A	chr11:5710656-5711961	GM12892	blood:	n/a	n/a
18	STAT3	chr11:5710627-5711227	GM12878	blood:	n/a	chr11:5710969-5710980 chr11:5710984-5710995 chr11:5710704-5710712 chr11:5710968-5710982
19	ATF2	chr11:5710628-5711278	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:5710756-5712586	GM12892	blood:	n/a	n/a
21	POLR2A	chr11:5710656-5712774	GM12878	blood:	n/a	n/a
22	SPI1	chr11:5710718-5711041	GM12878	blood:	n/a	chr11:5710846-5710859
23	SMC3	chr11:5710644-5711539	GM12878	blood:	n/a	n/a
24	MAZ	chr11:5710685-5711581	GM12878	blood:	n/a	n/a
25	POU2F2	chr11:5710765-5711282	GM12878	blood:	n/a	chr11:5710812-5710820
26	TAF1	chr11:5710839-5711269	H1-hESC	embryonic stem cell:	n/a	n/a
27	STAT3	chr11:5710806-5711155	MCF10A-Er-Src	breast:	n/a	chr11:5710969-5710980 chr11:5710984-5710995 chr11:5710968-5710982
28	POLR2A	chr11:5710822-5712031	U87	brain:	n/a	n/a
29	RUNX3	chr11:5710648-5711228	GM12878	blood:	n/a	n/a
30	TAF1	chr11:5710729-5711286	GM12878	blood:	n/a	n/a
31	EBF1	chr11:5710807-5711166	GM12878	blood:	n/a	chr11:5710914-5710924
32	POLR2A	chr11:5710628-5713120	GM19193	blood:	n/a	n/a
33	BCLAF1	chr11:5710744-5711152	GM12878	blood:	n/a	chr11:5710965-5710974
34	POLR2A	chr11:5710760-5711919	GM12891	blood:	n/a	n/a
35	POLR2A	chr11:5710722-5712429	IMR90	lung:	n/a	n/a
36	ZNF384	chr11:5710832-5711093	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:5710782-5712378	SK-N-SH	brain:	n/a	n/a
38	MXI1	chr11:5710615-5712221	GM12878	blood:	n/a	n/a
39	POLR2A	chr11:5710774-5711886	HUVEC	blood vessel:	n/a	n/a
40	RCOR1	chr11:5710716-5711633	GM12878	blood:	n/a	n/a
41	MTA3	chr11:5710607-5711712	GM12878	blood:	n/a	n/a
42	RELA	chr11:5710751-5712525	GM12891	blood:	n/a	n/a
43	KAP1	chr11:5710777-5711900	U2OS	brain:	n/a	n/a
44	POLR2A	chr11:5710747-5712397	HUVEC	blood vessel:	n/a	n/a
45	POU2F2	chr11:5710876-5711260	GM12878	blood:	n/a	n/a
46	POLR2A	chr11:5710757-5712493	GM12878	blood:	n/a	n/a
47	POLR2A	chr11:5710794-5711316	GM12878	blood:	n/a	n/a
48	STAT1	chr11:5710848-5711186	GM12878	blood:	n/a	chr11:5710984-5710995 chr11:5710968-5710982
49	POLR2A	chr11:5710344-5713953	GM12878	blood:	n/a	n/a
50	POLR2A	chr11:5710684-5712586	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:5706176..5707758-chr11:5710825..5713115,2	K562	blood:
2	11:4988858-5002113..11:5707362-5712027	Hela-S3	cervix:

Variant related genes	Relation type
TRIM5	TF binding region
TRIM22	TF binding region
ENSG00000225003	Chromatin interaction
ENSG00000132256	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs16934536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17305868	0.86[JPT][hapmap]
rs1995162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2343226	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2880575	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4992804	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57197373	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59386016	0.87[ASN][1000 genomes]
rs59723170	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72484712	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS 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	74 gene(s)	inside rSNPs	diseases
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	37 gene(s)	inside rSNPs	diseases
8	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
10	nsv896948	chr11:5701281-5719667	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2291841	TRIM22	cis	Muscle Skeletal	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5706200-5711000	Weak transcription	Gastric	stomach
2	chr11:5706400-5711000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:5706400-5711000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:5706400-5711000	Weak transcription	Lung	lung
5	chr11:5706600-5711000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:5706600-5711000	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:5706600-5711000	Weak transcription	Brain Substantia Nigra	brain
8	chr11:5706600-5711000	Weak transcription	Colonic Mucosa	Colon
9	chr11:5706600-5711000	Weak transcription	Fetal Heart	heart
10	chr11:5706800-5711000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:5706800-5711000	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:5706800-5711000	Weak transcription	Fetal Intestine Large	intestine
13	chr11:5706800-5711000	Weak transcription	Fetal Intestine Small	intestine
14	chr11:5706800-5711000	Weak transcription	Placenta	Placenta
15	chr11:5707200-5712200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:5709400-5711000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr11:5710200-5711000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:5710200-5711000	Weak transcription	Small Intestine	intestine
19	chr11:5710200-5711000	Flanking Active TSS	Dnd41	blood
20	chr11:5710200-5711000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr11:5710200-5711200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr11:5710200-5714000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:5710400-5711000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:5710400-5711000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:5710400-5712400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:5710400-5714000	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr11:5710400-5714000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr11:5710400-5714000	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr11:5710400-5714000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr11:5710600-5711000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:5710600-5711000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr11:5710600-5711000	Active TSS	Adipose Nuclei	Adipose
33	chr11:5710600-5711000	Enhancers	Liver	Liver
34	chr11:5710600-5711000	Flanking Active TSS	HMEC	breast
35	chr11:5710600-5711000	Flanking Active TSS	Osteobl	bone
36	chr11:5710600-5711200	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr11:5710600-5711200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:5710600-5711200	Enhancers	Fetal Stomach	stomach
39	chr11:5710600-5711400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr11:5710600-5711600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:5710600-5712400	Active TSS	Aorta	Aorta
42	chr11:5710600-5712400	Flanking Active TSS	HUVEC	blood vessel
43	chr11:5710600-5712600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr11:5710600-5712800	Active TSS	NHDF-Ad	bronchial
45	chr11:5710600-5713000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:5710600-5713000	Active TSS	GM12878-XiMat	blood
47	chr11:5710600-5713000	Active TSS	HSMM	muscle
48	chr11:5710600-5713400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr11:5710600-5713600	Active TSS	Brain Anterior Caudate	brain
50	chr11:5710600-5713600	Active TSS	Thymus	Thymus

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