Variant report

Variant	rs2278845
Chromosome Location	chr11:3829419-3829420
allele	C/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	chr11:3829170-3830159	HepG2	liver:	n/a	n/a
2	CTCF	chr11:3829027-3829460	GM12878	blood:	n/a	chr11:3829233-3829251
3	SMC3	chr11:3829076-3829455	HepG2	liver:	n/a	chr11:3829196-3829203
4	MXI1	chr11:3829202-3829452	K562	blood:	n/a	n/a
5	CHD2	chr11:3829160-3830082	Hela-S3	cervix:	n/a	n/a
6	ZBTB7A	chr11:3828991-3829923	K562	blood:	n/a	n/a
7	BHLHE40	chr11:3829202-3829575	GM12878	blood:	n/a	n/a
8	CTCF	chr11:3829098-3829524	GM19240	blood:	n/a	chr11:3829233-3829251
9	RAD21	chr11:3829046-3829513	H1-hESC	embryonic stem cell:	n/a	chr11:3829231-3829250
10	RAD21	chr11:3829012-3829559	A549	lung:	n/a	chr11:3829231-3829250
11	CHD2	chr11:3829101-3829660	H1-hESC	embryonic stem cell:	n/a	n/a
12	WRNIP1	chr11:3829093-3829596	GM12878	blood:	n/a	n/a
13	RAD21	chr11:3828888-3829914	HCT-116	colon:	n/a	chr11:3829231-3829250
14	SP1	chr11:3829143-3829886	H1-hESC	embryonic stem cell:	n/a	chr11:3829368-3829380 chr11:3829370-3829379 chr11:3829369-3829378 chr11:3829368-3829380 chr11:3829369-3829379 chr11:3829365-3829379
15	RAD21	chr11:3828968-3829432	IMR90	lung:	n/a	chr11:3829231-3829250
16	MYC	chr11:3829069-3830076	K562	blood:	n/a	n/a
17	CHD2	chr11:3829049-3829601	K562	blood:	n/a	n/a
18	MXI1	chr11:3828840-3831055	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr11:3829116-3830148	Hela-S3	cervix:	n/a	n/a
20	JUND	chr11:3829094-3829656	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr11:3829056-3829681	ECC-1	luminal epithelium:	n/a	n/a
22	TBP	chr11:3829044-3829957	H1-hESC	embryonic stem cell:	n/a	n/a
23	TRIM28	chr11:3829017-3829512	K562	blood:	n/a	n/a
24	CTCF	chr11:3828994-3829651	IMR90	lung:	n/a	chr11:3829233-3829251
25	MAZ	chr11:3829040-3830154	K562	blood:	n/a	n/a
26	TCF12	chr11:3828983-3829736	A549	lung:	n/a	n/a
27	YY1	chr11:3829166-3829546	ECC-1	luminal epithelium:	n/a	n/a
28	YY1	chr11:3829315-3829454	K562	blood:	n/a	n/a
29	CTCF	chr11:3829072-3829463	HepG2	liver:	n/a	chr11:3829233-3829251
30	TEAD4	chr11:3829037-3829630	K562	blood:	n/a	n/a
31	RCOR1	chr11:3829112-3829775	Hela-S3	cervix:	n/a	n/a
32	BHLHE40	chr11:3829131-3829420	K562	blood:	n/a	n/a
33	PML	chr11:3829191-3829723	GM12878	blood:	n/a	n/a
34	ZBTB7A	chr11:3829123-3829465	K562	blood:	n/a	n/a
35	FOXM1	chr11:3829108-3829497	GM12878	blood:	n/a	n/a
36	MAZ	chr11:3828967-3829476	HepG2	liver:	n/a	n/a
37	RAD21	chr11:3829035-3829434	Hela-S3	cervix:	n/a	chr11:3829231-3829250
38	ZC3H11A	chr11:3829084-3829624	K562	blood:	n/a	n/a
39	MXI1	chr11:3829178-3829780	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr11:3829122-3829439	Spleen_OC	spleen:	n/a	chr11:3829233-3829251
41	SMC3	chr11:3829064-3829557	GM12878	blood:	n/a	chr11:3829196-3829203
42	CTCF	chr11:3828847-3831006	SK-N-SH	brain:	n/a	chr11:3829233-3829251 chr11:3829946-3829959
43	MAX	chr11:3829091-3830179	K562	blood:	n/a	n/a
44	CTCF	chr11:3828943-3829550	K562	blood:	n/a	chr11:3829233-3829251
45	TBL1XR1	chr11:3829245-3829489	K562	blood:	n/a	n/a
46	SIN3A	chr11:3829071-3830154	H1-hESC	embryonic stem cell:	n/a	n/a
47	RAD21	chr11:3829000-3829493	HepG2	liver:	n/a	chr11:3829231-3829250
48	TBL1XR1	chr11:3829176-3829433	K562	blood:	n/a	n/a
49	POLR2A	chr11:3829092-3830177	K562	blood:	n/a	n/a
50	IRF1	chr11:3829138-3829966	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:3828900..3835031-chr11:3840756..3847684,8	K562	blood:
2	chr11:3829046..3832201-chr11:3860687..3864518,3	MCF-7	breast:
3	chr11:3827764..3831807-chr11:3860648..3864124,7	K562	blood:
4	chr11:3816139..3821205-chr11:3826361..3831544,11	MCF-7	breast:
5	chr11:3829231..3830814-chr11:4115429..4117638,2	K562	blood:

Variant related genes	Relation type
PGAP2	TF binding region
ENSG00000148985	Chromatin interaction
ENSG00000177105	Chromatin interaction
ENSG00000167325	Chromatin interaction
ENSG00000110713	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10767612	0.86[JPT][hapmap]
rs10835147	0.86[JPT][hapmap]
rs11602563	0.82[ASN][1000 genomes]
rs1530892	0.82[ASN][1000 genomes]
rs7117291	0.83[ASN][1000 genomes]
rs7946577	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1038220	chr11:3818041-3860024	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv1044882	chr11:3828986-3860024	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3828800-3830200	Active TSS	Fetal Kidney	kidney
2	chr11:3828800-3830600	Flanking Active TSS	Dnd41	blood
3	chr11:3829000-3829600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:3829000-3829600	Flanking Active TSS	Primary B cells from peripheral blood	blood
5	chr11:3829000-3829600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr11:3829000-3829600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr11:3829000-3829600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr11:3829000-3829600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr11:3829000-3829600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:3829000-3829600	Flanking Active TSS	Colonic Mucosa	Colon
11	chr11:3829000-3829600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
12	chr11:3829000-3829600	Flanking Active TSS	Fetal Muscle Leg	muscle
13	chr11:3829000-3829600	Flanking Active TSS	Fetal Thymus	thymus
14	chr11:3829000-3829600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr11:3829000-3829600	Flanking Active TSS	HUVEC	blood vessel
16	chr11:3829000-3829800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:3829000-3830000	Active TSS	Brain Hippocampus Middle	brain
18	chr11:3829000-3830000	Active TSS	Colon Smooth Muscle	Colon
19	chr11:3829000-3830000	Active TSS	Rectal Smooth Muscle	rectum
20	chr11:3829000-3830000	Active TSS	Right Ventricle	heart
21	chr11:3829000-3830200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:3829000-3830200	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr11:3829000-3830200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr11:3829000-3830200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:3829000-3830200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:3829000-3830200	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr11:3829000-3830200	Active TSS	Brain Anterior Caudate	brain
28	chr11:3829000-3830200	Active TSS	Brain Cingulate Gyrus	brain
29	chr11:3829000-3830200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:3829000-3830200	Active TSS	Brain Substantia Nigra	brain
31	chr11:3829000-3830200	Active TSS	A549	lung
32	chr11:3829000-3830400	Active TSS	H1 Cell Line	embryonic stem cell
33	chr11:3829000-3830400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr11:3829000-3830400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:3829000-3830400	Active TSS	Fetal Lung	lung
36	chr11:3829000-3830400	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr11:3829000-3830600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr11:3829000-3830600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr11:3829000-3830600	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr11:3829000-3830600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr11:3829000-3830600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:3829000-3830800	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr11:3829000-3830800	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr11:3829000-3830800	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr11:3829200-3829600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr11:3829200-3829600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:3829200-3829600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr11:3829200-3829600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr11:3829200-3829600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:3829200-3829600	Flanking Active TSS	Brain Germinal Matrix	brain

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