Variant report

Variant	rs11666503
Chromosome Location	chr19:53427209-53427210
allele	C/T
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	chr19:53426001-53427721	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:53426120-53427633	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr19:53426110-53427803	K562	blood:	n/a	n/a
4	MYC	chr19:53426201-53427253	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr19:53426994-53427725	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:53427172-53427826	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:53425948-53427245	MCF-7	breast:	n/a	n/a
8	CEBPB	chr19:53427010-53427373	H1-hESC	embryonic stem cell:	n/a	chr19:53427191-53427202
9	CEBPB	chr19:53426972-53427395	ECC-1	luminal epithelium:	n/a	chr19:53427191-53427202
10	CTCF	chr19:53427141-53427798	K562	blood:	n/a	n/a
11	POLR2A	chr19:53425844-53427535	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr19:53425700-53427967	K562	blood:	n/a	n/a
13	CEBPB	chr19:53426868-53427409	K562	blood:	n/a	chr19:53427191-53427202
14	CEBPB	chr19:53427031-53427282	K562	blood:	n/a	chr19:53427191-53427202
15	CEBPB	chr19:53427009-53427387	HepG2	liver:	n/a	chr19:53427191-53427202
16	POLR2A	chr19:53427076-53427814	HL-60	blood:	n/a	n/a
17	FOS	chr19:53427098-53427357	MCF10A-Er-Src	breast:	n/a	n/a
18	CEBPB	chr19:53427096-53427246	HepG2	liver:	n/a	chr19:53427191-53427202
19	POLR2A	chr19:53426124-53429666	K562	blood:	n/a	n/a
20	POLR2A	chr19:53426092-53427668	GM12878	blood:	n/a	n/a
21	CEBPB	chr19:53427022-53427356	IMR90	lung:	n/a	chr19:53427191-53427202
22	CEBPB	chr19:53426302-53427395	Hela-S3	cervix:	n/a	chr19:53427191-53427202
23	CEBPB	chr19:53427108-53427414	ECC-1	luminal epithelium:	n/a	chr19:53427191-53427202
24	POLR2A	chr19:53426002-53427790	PANC-1	pancreas:	n/a	n/a
25	CEBPB	chr19:53427057-53427283	HepG2	liver:	n/a	chr19:53427191-53427202
26	JUN	chr19:53426087-53428013	K562	blood:	n/a	chr19:53426810-53426819 chr19:53426463-53426472 chr19:53426616-53426624
27	POLR2A	chr19:53425901-53427685	PBDE	blood:	n/a	n/a
28	SMC3	chr19:53427105-53427355	HepG2	liver:	n/a	n/a
29	CEBPB	chr19:53426991-53427679	K562	blood:	n/a	chr19:53427191-53427202
30	POLR2A	chr19:53426973-53427774	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:53426133..53428140-chr19:53445241..53446971,2	K562	blood:
2	chr19:53398338..53401958-chr19:53425181..53428572,6	K562	blood:
3	chr19:53425636..53428538-chr19:53430721..53433929,3	K562	blood:
4	chr19:53426133..53428640-chr19:53444456..53447019,4	K562	blood:
5	chr19:53418400..53422745-chr19:53423096..53427800,7	K562	blood:
6	chr19:53399773..53402425-chr19:53424830..53427617,2	MCF-7	breast:
7	chr19:53398338..53403121-chr19:53425170..53428184,6	K562	blood:
8	chr19:53424791..53427731-chr19:53464365..53467863,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VN1R2-12	chr19:53426926-53427328	ENSG00000269646.1

Variant related genes	Relation type
ZNF888	TF binding region
ENSG00000213793	Chromatin interaction
ENSG00000213801	Chromatin interaction
ENSG00000182986	Chromatin interaction
ENSG00000221874	Chromatin interaction
ENSG00000180257	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11667788	0.92[ASN][1000 genomes]
rs12609561	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12972851	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1978620	0.84[ASN][1000 genomes]
rs4334054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56182098	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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 target site	32 gene(s)	inside rSNPs	diseases
4	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv912318	chr19:53118278-53451291	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv432072	chr19:53144788-53554388	Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	esv3401212	chr19:53151131-53482063	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv912321	chr19:53186836-53451291	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv1058903	chr19:53193570-53489633	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1067280	chr19:53193570-53567287	Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	nsv544062	chr19:53193570-53567287	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv580030	chr19:53194344-53547394	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
16	nsv1057118	chr19:53195426-53480449	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
17	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	43 gene(s)	inside rSNPs	diseases
18	nsv912323	chr19:53249347-53451291	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
19	esv3431689	chr19:53291230-53483998	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
20	nsv912329	chr19:53317001-53440653	Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
21	nsv912330	chr19:53317001-53478109	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
22	nsv1064234	chr19:53346827-53480449	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
23	esv3319159	chr19:53361167-53446431	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
24	esv3319160	chr19:53361308-53446343	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers 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 miRNA target site	13 gene(s)	inside rSNPs	diseases
25	nsv912340	chr19:53370345-53430362	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription 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 target site	11 gene(s)	inside rSNPs	diseases
26	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
27	nsv963071	chr19:53401720-53480869	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
28	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
29	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
30	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
31	nsv522421	chr19:53413825-53433054	Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53425600-53427400	Active TSS	NHDF-Ad	bronchial
2	chr19:53425600-53427800	Active TSS	Rectal Smooth Muscle	rectum
3	chr19:53425800-53427400	Active TSS	Brain Anterior Caudate	brain
4	chr19:53425800-53427600	Active TSS	NHLF	lung
5	chr19:53425800-53427800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:53425800-53427800	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr19:53426000-53427400	Active TSS	Brain Angular Gyrus	brain
8	chr19:53426000-53427600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr19:53426000-53427600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:53426200-53427400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:53426200-53427400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr19:53426200-53427400	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr19:53426200-53427400	Active TSS	Colon Smooth Muscle	Colon
14	chr19:53426200-53427400	Active TSS	Right Atrium	heart
15	chr19:53426400-53427600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:53426400-53427600	Active TSS	Brain Hippocampus Middle	brain
17	chr19:53426600-53427800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:53426600-53444800	Weak transcription	Fetal Heart	heart
19	chr19:53426800-53427400	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr19:53426800-53427400	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr19:53426800-53427800	Enhancers	Fetal Brain Male	brain
22	chr19:53426800-53427800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr19:53426800-53428200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:53426800-53431600	Weak transcription	HSMMtube	muscle
25	chr19:53426800-53432400	Weak transcription	Gastric	stomach
26	chr19:53426800-53434200	Weak transcription	NH-A	brain
27	chr19:53426800-53435600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:53426800-53444800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr19:53426800-53445000	Weak transcription	Small Intestine	intestine
30	chr19:53426800-53445200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:53426800-53445200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:53427000-53427400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr19:53427000-53427400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr19:53427000-53427400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr19:53427000-53427400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:53427000-53427400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:53427000-53427400	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr19:53427000-53427400	Flanking Active TSS	Stomach Mucosa	stomach
39	chr19:53427000-53427400	Enhancers	GM12878-XiMat	blood
40	chr19:53427000-53427400	Enhancers	HMEC	breast
41	chr19:53427000-53427600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr19:53427000-53427600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr19:53427000-53427600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr19:53427000-53427600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr19:53427000-53427600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr19:53427000-53427600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr19:53427000-53427600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr19:53427000-53427600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr19:53427000-53427600	Flanking Active TSS	Dnd41	blood
50	chr19:53427000-53427800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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