Variant report

Variant	rs11886092
Chromosome Location	chr2:20063674-20063675
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	CTCF	chr2:20063624-20063750	MCF-7	breast:	n/a	n/a
2	TBP	chr2:20063006-20063820	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF2	chr2:20063190-20063678	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAFK	chr2:20063624-20063758	HepG2	liver:	n/a	n/a
5	RAD21	chr2:20062332-20063915	SK-N-SH	brain:	n/a	chr2:20063384-20063398 chr2:20063312-20063331 chr2:20063687-20063699
6	CTCF	chr2:20063660-20063810	HA-sp	spinal cord:	n/a	n/a
7	CTCF	chr2:20063620-20063759	MCF-7	breast:	n/a	n/a
8	SMC3	chr2:20062334-20063863	SK-N-SH	brain:	n/a	chr2:20063398-20063408 chr2:20063689-20063699 chr2:20063316-20063330
9	MAX	chr2:20062779-20063923	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr2:20062677-20063891	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr2:20062968-20063822	HepG2	liver:	n/a	chr2:20063384-20063398 chr2:20063312-20063331 chr2:20063687-20063699
12	TAF7	chr2:20063043-20063814	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chr2:20062992-20063894	H1-hESC	embryonic stem cell:	n/a	chr2:20063384-20063398 chr2:20063312-20063331 chr2:20063687-20063699
14	CTCF	chr2:20063592-20063786	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr2:20062950-20063836	H1-hESC	embryonic stem cell:	n/a	chr2:20063314-20063332 chr2:20063309-20063330 chr2:20063315-20063331
16	RFX5	chr2:20063175-20063718	HepG2	liver:	n/a	n/a
17	RAD21	chr2:20062947-20063845	HepG2	liver:	n/a	chr2:20063384-20063398 chr2:20063312-20063331 chr2:20063687-20063699
18	CTCF	chr2:20063580-20063730	GM12869	blood:	n/a	n/a
19	CTCF	chr2:20063658-20063749	MCF-7	breast:	n/a	n/a
20	YY1	chr2:20063099-20063815	HepG2	liver:	n/a	n/a
21	BHLHE40	chr2:20063129-20063833	HepG2	liver:	n/a	n/a
22	TBP	chr2:20063413-20063719	HepG2	liver:	n/a	n/a
23	CTCF	chr2:20063560-20063710	WERI-Rb-1	eye:	n/a	n/a
24	POLR2A	chr2:20063419-20063796	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr2:20062928-20063876	MCF-7	breast:	n/a	chr2:20063314-20063332 chr2:20063309-20063330 chr2:20063315-20063331
26	CHD2	chr2:20062879-20063755	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr2:20063640-20063790	NHLF	lung:	n/a	n/a
28	MAX	chr2:20062881-20063860	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr2:20063131-20063763	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr2:20063520-20063828	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr2:20063660-20063698	GM12891	blood:	n/a	n/a
32	RAD21	chr2:20062875-20063925	H1-hESC	embryonic stem cell:	n/a	chr2:20063384-20063398 chr2:20063312-20063331 chr2:20063687-20063699
33	CTCF	chr2:20063660-20063810	WERI-Rb-1	eye:	n/a	n/a
34	CHD1	chr2:20063005-20063758	IMR90	lung:	n/a	n/a
35	RAD21	chr2:20062873-20063690	MCF-7	breast:	n/a	chr2:20063384-20063398 chr2:20063312-20063331
36	MBD4	chr2:20063018-20063889	HepG2	liver:	n/a	n/a
37	ZNF143	chr2:20063006-20063763	H1-hESC	embryonic stem cell:	n/a	chr2:20063456-20063474
38	CTCF	chr2:20063640-20063790	GM12870	blood:	n/a	n/a
39	CTCF	chr2:20062380-20063761	A549	lung:	n/a	chr2:20063314-20063332 chr2:20063309-20063330 chr2:20063315-20063331
40	MYBL2	chr2:20062939-20063681	HepG2	liver:	n/a	n/a
41	MYC	chr2:20063142-20063692	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr2:20063540-20063690	HepG2	liver:	n/a	n/a
43	CTCF	chr2:20063559-20063808	HepG2	liver:	n/a	n/a
44	MXI1	chr2:20062880-20063695	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr2:20062962-20063831	H1-hESC	embryonic stem cell:	n/a	chr2:20063384-20063398 chr2:20063312-20063331 chr2:20063687-20063699
46	MAX	chr2:20062648-20063874	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr2:20063640-20063751	HepG2	liver:	n/a	n/a
48	CTCF	chr2:20062789-20063890	SK-N-SH	brain:	n/a	chr2:20063314-20063332 chr2:20063309-20063330 chr2:20063315-20063331
49	RAD21	chr2:20062782-20063760	HCT-116	colon:	n/a	chr2:20063384-20063398 chr2:20063312-20063331 chr2:20063687-20063699
50	CTCF	chr2:20063600-20063750	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:19968930..19969804-chr2:20062834..20063763,3	MCF-7	breast:
2	chr2:18663724..18664634-chr2:20062948..20063698,3	MCF-7	breast:
3	chr2:19592208..19593951-chr2:20061932..20064637,2	MCF-7	breast:
4	chr2:18616431..18616984-chr2:20063230..20063754,2	K562	blood:
5	chr2:20063399..20066786-chr2:20072740..20074746,3	K562	blood:
6	chr2:18701353..18702868-chr2:20062861..20063796,5	K562	blood:
7	chr2:18568690..18569227-chr2:20063102..20063706,2	MCF-7	breast:
8	chr2:20060793..20063745-chr2:20067045..20068888,2	MCF-7	breast:
9	chr2:20063170..20065730-chr2:20100500..20102018,2	MCF-7	breast:
10	chr2:19568949..19569749-chr2:20062849..20063723,3	MCF-7	breast:

Variant related genes	Relation type
LINC00954	TF binding region
ENSG00000271991	Chromatin interaction
ENSG00000228784	Chromatin interaction
ENSG00000183891	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs13002069	0.81[AMR][1000 genomes]
rs13028359	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35487326	0.85[AFR][1000 genomes]
rs4439914	0.84[CEU][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873711	chr2:19950864-20073860	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
4	nsv455819	chr2:19987440-20095690	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv581155	chr2:19987440-20095690	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
7	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20060600-20065200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:20062200-20066600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:20062200-20068200	Weak transcription	NHDF-Ad	bronchial
4	chr2:20062400-20063800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr2:20063000-20063800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:20063000-20063800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr2:20063000-20063800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr2:20063000-20063800	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr2:20063000-20063800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:20063000-20063800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:20063000-20063800	Enhancers	Esophagus	oesophagus
12	chr2:20063000-20063800	Enhancers	Pancreas	Pancrea
13	chr2:20063000-20065200	Enhancers	Fetal Thymus	thymus
14	chr2:20063000-20065600	Enhancers	GM12878-XiMat	blood
15	chr2:20063200-20063800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr2:20063200-20063800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:20063200-20063800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:20063200-20063800	Enhancers	Brain Anterior Caudate	brain
19	chr2:20063200-20063800	Enhancers	Brain Germinal Matrix	brain
20	chr2:20063200-20063800	Enhancers	Gastric	stomach
21	chr2:20063200-20063800	Enhancers	Ovary	ovary
22	chr2:20063200-20063800	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr2:20063400-20063800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr2:20063400-20063800	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr2:20063400-20063800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:20063400-20063800	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr2:20063400-20063800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr2:20063400-20063800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:20063400-20063800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:20063400-20063800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:20063400-20063800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:20063400-20063800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:20063400-20063800	Flanking Active TSS	Liver	Liver
34	chr2:20063400-20063800	Active TSS	Brain Angular Gyrus	brain
35	chr2:20063400-20063800	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr2:20063400-20063800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr2:20063400-20063800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:20063400-20063800	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr2:20063400-20063800	Flanking Active TSS	Colonic Mucosa	Colon
40	chr2:20063400-20063800	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr2:20063400-20063800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
42	chr2:20063400-20063800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr2:20063400-20063800	Enhancers	Fetal Brain Male	brain
44	chr2:20063400-20063800	Enhancers	Fetal Heart	heart
45	chr2:20063400-20063800	Enhancers	Fetal Muscle Leg	muscle
46	chr2:20063400-20063800	Enhancers	Left Ventricle	heart
47	chr2:20063400-20063800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr2:20063400-20063800	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr2:20063400-20063800	Enhancers	Right Atrium	heart
50	chr2:20063400-20063800	Flanking Active TSS	Right Ventricle	heart

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