Variant report

Variant	rs61896956
Chromosome Location	chr11:3829862-3829863
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:103)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:103 , 50 per page) page: 1 2 3

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	MAX	chr11:3829752-3830019	K562	blood:	n/a	n/a
3	POLR2A	chr11:3829743-3830033	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr11:3829820-3829970	AG04449	skin:	n/a	chr11:3829946-3829959
5	CHD2	chr11:3829160-3830082	Hela-S3	cervix:	n/a	n/a
6	ZBTB7A	chr11:3828991-3829923	K562	blood:	n/a	n/a
7	POLR2A	chr11:3829718-3829999	MCF-7	breast:	n/a	n/a
8	UBTF	chr11:3829716-3829910	K562	blood:	n/a	n/a
9	EGR1	chr11:3829569-3829933	K562	blood:	n/a	n/a
10	ELF1	chr11:3829552-3829998	K562	blood:	n/a	n/a
11	POLR2A	chr11:3829760-3829983	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr11:3828888-3829914	HCT-116	colon:	n/a	chr11:3829231-3829250
13	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
14	MAZ	chr11:3829713-3830717	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:3829436-3830081	PFSK-1	brain:	n/a	n/a
16	ELF1	chr11:3829553-3829918	K562	blood:	n/a	n/a
17	ZBTB7A	chr11:3829489-3829921	HepG2	liver:	n/a	n/a
18	POLR2A	chr11:3829559-3830005	HepG2	liver:	n/a	n/a
19	CTCF	chr11:3829720-3829870	HRPEpiC	eye:	n/a	n/a
20	ZNF143	chr11:3829795-3829924	H1-hESC	embryonic stem cell:	n/a	n/a
21	MYC	chr11:3829069-3830076	K562	blood:	n/a	n/a
22	MXI1	chr11:3828840-3831055	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr11:3829116-3830148	Hela-S3	cervix:	n/a	n/a
24	TBP	chr11:3829044-3829957	H1-hESC	embryonic stem cell:	n/a	n/a
25	SIN3AK20	chr11:3829735-3830198	H1-hESC	embryonic stem cell:	n/a	n/a
26	HEY1	chr11:3829721-3830023	K562	blood:	n/a	n/a
27	MAZ	chr11:3829040-3830154	K562	blood:	n/a	n/a
28	MAX	chr11:3829750-3830235	ECC-1	luminal epithelium:	n/a	n/a
29	HEY1	chr11:3829436-3830095	HepG2	liver:	n/a	n/a
30	MAZ	chr11:3829562-3830034	GM12878	blood:	n/a	n/a
31	ZBTB7A	chr11:3829527-3830097	K562	blood:	n/a	n/a
32	MYC	chr11:3829714-3829914	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr11:3828847-3831006	SK-N-SH	brain:	n/a	chr11:3829233-3829251 chr11:3829946-3829959
34	MAX	chr11:3829091-3830179	K562	blood:	n/a	n/a
35	SIN3A	chr11:3829071-3830154	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr11:3829092-3830177	K562	blood:	n/a	n/a
37	IRF1	chr11:3829138-3829966	K562	blood:	n/a	n/a
38	CTCF	chr11:3829860-3830010	GM12872	blood:	n/a	chr11:3829946-3829959
39	POLR2A	chr11:3829783-3829991	GM12878	blood:	n/a	n/a
40	POLR2A	chr11:3829470-3830081	GM18951	blood:	n/a	n/a
41	HEY1	chr11:3829781-3830071	K562	blood:	n/a	n/a
42	EBF1	chr11:3829732-3830048	GM12878	blood:	n/a	n/a
43	TAF1	chr11:3829046-3830010	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr11:3829230-3830015	HepG2	liver:	n/a	n/a
45	MAX	chr11:3829006-3830808	A549	lung:	n/a	chr11:3830582-3830592
46	TAF1	chr11:3829557-3829944	K562	blood:	n/a	n/a
47	POLR2A	chr11:3829130-3830108	ECC-1	luminal epithelium:	n/a	n/a
48	SMC3	chr11:3829848-3829993	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr11:3829211-3830035	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr11:3829783-3829929	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:3829824-3829874	IMR90	lung:	fetal
2	chr11:3829824-3829874	NHDF-neo	bronchial:	n/a
3	chr11:3829824-3829874	Hela-S3	cervix:	n/a
4	chr11:3829824-3829874	MCF10A-Er-Src	breast:	n/a
5	chr11:3829824-3829874	SAEC	small airway:	n/a
6	chr11:3829824-3829874	SKMC	muscle:	n/a
7	chr11:3829824-3829874	AG04449	skin:	fetal
8	chr11:3829824-3829874	GM12892	blood:	n/a
9	chr11:3829824-3829874	PFSK-1	brain:	n/a
10	chr11:3829824-3829874	HUVEC	blood vessel:	n/a
11	chr11:3829824-3829874	CMK	blood:	n/a
12	chr11:3829824-3829874	HRCEpiC	kidney:	n/a
13	chr11:3829824-3829874	HPAEpiC	pulmonary alveolar:	n/a
14	chr11:3829824-3829874	SK-N-SH	brain:	n/a
15	chr11:3829824-3829874	PANC-1	pancreas:	n/a
16	chr11:3829824-3829874	HRPEpiC	eye:	n/a
17	chr11:3829824-3829874	GM12891	blood:	n/a
18	chr11:3829824-3829874	HCM	heart:	n/a
19	chr11:3829824-3829874	HepG2	liver:	n/a
20	chr11:3829824-3829874	HMEC	breast:	n/a
21	chr11:3829824-3829874	HRE	kidney:	n/a
22	chr11:3829824-3829874	PrEC	prostate:	n/a
23	chr11:3829824-3829874	GM06990	blood:	n/a
24	chr11:3829824-3829874	HNPCEpiC	eye:	n/a
25	chr11:3829824-3829874	AoSMC	blood vessel:	n/a
26	chr11:3829824-3829874	HEK293	kidney:	embryo
27	chr11:3829824-3829874	HCF	heart:	n/a
28	chr11:3829824-3829874	HCT-116	colon:	n/a
29	chr11:3829824-3829874	AG10803	skin:	n/a
30	chr11:3829824-3829874	GM12878	blood:	n/a
31	chr11:3829824-3829874	NHBE	bronchial:	n/a
32	chr11:3829824-3829874	GM19239	blood:	n/a
33	chr11:3829824-3829874	AG09319	gingival:	n/a
34	chr11:3829824-3829874	K562	blood:	n/a
35	chr11:3829824-3829874	A549	lung:	n/a
36	chr11:3829824-3829874	T-47D	breast:	n/a
37	chr11:3829824-3829874	ovcar-3	ovarian:	n/a
38	chr11:3829824-3829874	HL-60	blood:	n/a
39	chr11:3829824-3829874	SK-N-MC	brain:	n/a
40	chr11:3829824-3829874	HIPEpiC	eye:	n/a
41	chr11:3829824-3829874	ProgFib	skin:	n/a
42	chr11:3829824-3829874	BJ	skin:	n/a
43	chr11:3829824-3829874	HAEpiC	amniotic membrane:	n/a
44	chr11:3829824-3829874	NH-A	brain:	n/a
45	chr11:3829824-3829874	HEEpiC	esophagus:	n/a
46	chr11:3829824-3829874	LNCaP	prostate:	n/a
47	chr11:3829824-3829874	HCPEpiC	choroid plexus:	n/a
48	chr11:3829824-3829874	Hepatocyte	liver:	n/a
49	chr11:3829824-3829874	Jurkat	blood:	n/a
50	chr11:3829824-3829874	AG04450	lung:	fetal

(count:7 , 50 per page) page: 1

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	chr11:3829597..3830296-chr11:3845729..3846607,3	K562	blood:
6	chr11:3829231..3830814-chr11:4115429..4117638,2	K562	blood:
7	chr11:3829786..3831602-chr11:3876105..3877704,2	K562	blood:

No data

Variant related genes	Relation type
PGAP2	TF binding region
PGAP2	CpG island
ENSG00000167325	Chromatin interaction
ENSG00000110713	Chromatin interaction
ENSG00000228661	Chromatin interaction
ENSG00000177105	Chromatin interaction
ENSG00000263421	Chromatin interaction
ENSG00000148985	Chromatin interaction
ENSG00000167323	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1049388	1.00[ASN][1000 genomes]
rs11029983	1.00[ASN][1000 genomes]
rs11030043	1.00[ASN][1000 genomes]
rs11030044	1.00[ASN][1000 genomes]
rs11030055	1.00[ASN][1000 genomes]
rs11030173	1.00[ASN][1000 genomes]
rs11600857	1.00[ASN][1000 genomes]
rs11606318	1.00[ASN][1000 genomes]
rs11606483	1.00[ASN][1000 genomes]
rs17173882	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191448	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276405	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276453	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910577	1.00[ASN][1000 genomes]
rs4910846	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910852	1.00[ASN][1000 genomes]
rs4910856	1.00[ASN][1000 genomes]
rs4910857	1.00[ASN][1000 genomes]
rs61896929	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896930	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896931	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896953	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896954	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896957	1.00[ASN][1000 genomes]
rs61896958	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896959	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899361	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899362	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899363	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899392	1.00[ASN][1000 genomes]
rs61899393	1.00[ASN][1000 genomes]
rs6578414	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101788	1.00[ASN][1000 genomes]
rs72844340	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844341	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430467	1.00[ASN][1000 genomes]
rs74050940	1.00[ASN][1000 genomes]

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	chr11:3829000-3830000	Active TSS	Brain Hippocampus Middle	brain
4	chr11:3829000-3830000	Active TSS	Colon Smooth Muscle	Colon
5	chr11:3829000-3830000	Active TSS	Rectal Smooth Muscle	rectum
6	chr11:3829000-3830000	Active TSS	Right Ventricle	heart
7	chr11:3829000-3830200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:3829000-3830200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr11:3829000-3830200	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr11:3829000-3830200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:3829000-3830200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr11:3829000-3830200	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr11:3829000-3830200	Active TSS	Brain Anterior Caudate	brain
14	chr11:3829000-3830200	Active TSS	Brain Cingulate Gyrus	brain
15	chr11:3829000-3830200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:3829000-3830200	Active TSS	Brain Substantia Nigra	brain
17	chr11:3829000-3830200	Active TSS	A549	lung
18	chr11:3829000-3830400	Active TSS	H1 Cell Line	embryonic stem cell
19	chr11:3829000-3830400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr11:3829000-3830400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:3829000-3830400	Active TSS	Fetal Lung	lung
22	chr11:3829000-3830400	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr11:3829000-3830600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr11:3829000-3830600	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr11:3829000-3830600	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr11:3829000-3830600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr11:3829000-3830600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:3829000-3830800	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr11:3829000-3830800	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr11:3829000-3830800	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr11:3829200-3830000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:3829200-3830000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:3829200-3830000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:3829200-3830000	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr11:3829200-3830000	Active TSS	Fetal Intestine Large	intestine
36	chr11:3829200-3830000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr11:3829200-3830000	Active TSS	HSMMtube	muscle
38	chr11:3829200-3830200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr11:3829200-3830200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr11:3829200-3830200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:3829200-3830200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:3829200-3830200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:3829200-3830200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:3829200-3830200	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr11:3829200-3830200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:3829200-3830200	Active TSS	Aorta	Aorta
47	chr11:3829200-3830200	Active TSS	Fetal Intestine Small	intestine
48	chr11:3829200-3830200	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr11:3829200-3830200	Active TSS	Gastric	stomach
50	chr11:3829200-3830200	Active TSS	Lung	lung

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