Variant report

Variant	rs11886025
Chromosome Location	chr2:98279076-98279077
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	chr2:98278939-98281047	HepG2	liver:	n/a	n/a
2	EBF1	chr2:98279015-98280866	GM12878	blood:	n/a	chr2:98279203-98279214 chr2:98279203-98279216
3	TEAD4	chr2:98279054-98280052	HepG2	liver:	n/a	chr2:98279746-98279755
4	POLR2A	chr2:98277387-98280171	K562	blood:	n/a	n/a
5	RELA	chr2:98279075-98281449	GM15510	blood:	n/a	n/a
6	POLR2A	chr2:98278878-98281363	K562	blood:	n/a	n/a
7	POLR2A	chr2:98277968-98281074	GM12892	blood:	n/a	n/a
8	CTCF	chr2:98279051-98279101	HepG2	liver:	n/a	n/a
9	ZNF143	chr2:98278942-98279088	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr2:98278131-98281374	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr2:98278940-98279090	HAc	cerebellar:	n/a	chr2:98279033-98279046
12	CTCF	chr2:98279000-98279150	HCPEpiC	choroid plexus:	n/a	chr2:98279033-98279046
13	HCFC1	chr2:98278895-98281591	Hela-S3	cervix:	n/a	n/a
14	NFATC1	chr2:98279001-98280035	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:98279047-98280991	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:98278016-98282070	HepG2	liver:	n/a	n/a
17	EBF1	chr2:98278965-98279557	GM12878	blood:	n/a	chr2:98279203-98279214 chr2:98279203-98279216
18	TCF7L2	chr2:98278967-98279455	HEK293	kidney:	n/a	n/a
19	POLR2A	chr2:98278955-98281018	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr2:98279073-98281166	HL-60	blood:	n/a	n/a
21	POLR2A	chr2:98279023-98281134	GM12892	blood:	n/a	n/a
22	CHD1	chr2:98278816-98281671	IMR90	lung:	n/a	chr2:98280105-98280115
23	POLR2A	chr2:98278925-98281009	GM12891	blood:	n/a	n/a
24	CTCF	chr2:98278862-98281848	SK-N-SH	brain:	n/a	chr2:98280555-98280563 chr2:98280387-98280400 chr2:98279033-98279046 chr2:98279295-98279308
25	POLR2A	chr2:98279071-98280971	GM12892	blood:	n/a	n/a
26	POLR2A	chr2:98278890-98281152	SK-N-MC	brain:	n/a	n/a
27	RFX5	chr2:98278853-98281707	SK-N-SH	brain:	n/a	chr2:98280645-98280659
28	WRNIP1	chr2:98278648-98280144	GM12878	blood:	n/a	n/a
29	CTCF	chr2:98278980-98279130	HBMEC	blood vessel:	n/a	chr2:98279033-98279046
30	POLR2A	chr2:98279061-98281010	GM12878	blood:	n/a	n/a
31	MAX	chr2:98279019-98281346	GM12878	blood:	n/a	chr2:98280224-98280234 chr2:98279386-98279396
32	POLR2A	chr2:98277989-98281149	GM12878	blood:	n/a	n/a
33	MTA3	chr2:98278702-98280226	GM12878	blood:	n/a	n/a
34	RCOR1	chr2:98278984-98281553	K562	blood:	n/a	n/a
35	POLR2A	chr2:98279072-98281133	K562	blood:	n/a	n/a
36	POLR2A	chr2:98279042-98281164	K562	blood:	n/a	n/a
37	TCF7L2	chr2:98279010-98279909	Hela-S3	cervix:	n/a	chr2:98279469-98279478
38	CTCF	chr2:98278940-98279090	GM12874	blood:	n/a	chr2:98279033-98279046
39	RUNX3	chr2:98279013-98280941	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:98278795-98281292	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:98278623-98281994	K562	blood:	n/a	n/a
42	PML	chr2:98278989-98281299	GM12878	blood:	n/a	chr2:98279470-98279479
43	MAX	chr2:98279063-98281291	A549	lung:	n/a	chr2:98280224-98280234 chr2:98279386-98279396
44	POLR2A	chr2:98279047-98281239	GM18505	blood:	n/a	n/a
45	RAD21	chr2:98278918-98279083	H1-hESC	embryonic stem cell:	n/a	chr2:98279032-98279045
46	POLR2A	chr2:98278923-98280972	GM12892	blood:	n/a	n/a
47	POLR2A	chr2:98278714-98281017	HepG2	liver:	n/a	n/a
48	ATF2	chr2:98279062-98279869	GM12878	blood:	n/a	n/a
49	POLR2A	chr2:98278898-98281207	U87	brain:	n/a	n/a
50	POLR2A	chr2:98278471-98280317	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:98205848..98207835-chr2:98279004..98283186,3	MCF-7	breast:
2	chr2:98278220..98280235-chr2:98364964..98367550,2	K562	blood:
3	chr2:98277235..98279650-chr2:98312622..98314344,2	K562	blood:
4	chr2:98277787..98279697-chr2:98287927..98289913,2	MCF-7	breast:
5	chr2:98278667..98281978-chr2:98283382..98286512,4	K562	blood:
6	chr2:98278665..98281371-chr2:98305087..98308005,4	MCF-7	breast:
7	chr2:98277609..98280060-chr2:98302722..98304227,2	MCF-7	breast:

Variant related genes	Relation type
ACTR1B	TF binding region
LINC01125	TF binding region
ENSG00000196912	Chromatin interaction
ENSG00000228486	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11886239	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904110	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17022045	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3475	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55981050	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59134572	0.92[ASN][1000 genomes]
rs6543021	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745653	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72951131	0.80[AMR][1000 genomes]
rs73959752	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73959753	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73959769	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73959786	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73959787	0.85[EUR][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	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	nsv431402	chr2:97669032-98281634	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1005846	chr2:97972600-98281634	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv1009263	chr2:98013814-98281634	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98275400-98279200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:98276000-98279400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:98276200-98279200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:98277400-98279400	Weak transcription	Aorta	Aorta
5	chr2:98277600-98279200	Enhancers	Pancreas	Pancrea
6	chr2:98277600-98279400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr2:98277800-98279200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:98277800-98279600	Enhancers	Spleen	Spleen
9	chr2:98277800-98279800	Flanking Active TSS	Brain Angular Gyrus	brain
10	chr2:98278000-98279200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:98278000-98279200	Enhancers	Brain Substantia Nigra	brain
12	chr2:98278000-98279200	Enhancers	Fetal Brain Male	brain
13	chr2:98278000-98279800	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr2:98278000-98279800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:98278000-98279800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr2:98278200-98279200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:98278200-98279200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:98278200-98279400	Enhancers	Stomach Mucosa	stomach
19	chr2:98278200-98279400	Flanking Active TSS	NHDF-Ad	bronchial
20	chr2:98278200-98280000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr2:98278200-98280000	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr2:98278400-98279200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:98278400-98279200	Enhancers	Fetal Lung	lung
24	chr2:98278400-98279400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:98278400-98279400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:98278400-98279400	Enhancers	Placenta	Placenta
27	chr2:98278400-98279400	Enhancers	Gastric	stomach
28	chr2:98278400-98279400	Flanking Active TSS	Rectal Smooth Muscle	rectum
29	chr2:98278400-98279400	Flanking Active TSS	Hela-S3	cervix
30	chr2:98278400-98279600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:98278400-98279800	Flanking Active TSS	K562	blood
32	chr2:98278400-98280200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:98278600-98279200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr2:98278600-98279200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr2:98278600-98279200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:98278600-98279200	Flanking Active TSS	HepG2	liver
37	chr2:98278600-98279200	Flanking Active TSS	NHLF	lung
38	chr2:98278600-98279400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr2:98278600-98279400	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr2:98278600-98279400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:98278600-98279400	Flanking Active TSS	Right Ventricle	heart
42	chr2:98278600-98279600	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr2:98278600-98279600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr2:98278600-98279800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:98278600-98279800	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr2:98278600-98279800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr2:98278600-98279800	Flanking Active TSS	Thymus	Thymus
48	chr2:98278600-98279800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr2:98278600-98280000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr2:98278600-98280000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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