Variant report

Variant	rs16988425
Chromosome Location	chr22:30634918-30634919
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	NR3C1	chr22:30634705-30635078	A549	lung:	n/a	n/a
2	POLR2A	chr22:30634332-30646592	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr22:30634608-30635258	A549	lung:	n/a	n/a
4	TCF12	chr22:30634411-30635066	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr22:30633649-30636107	A549	lung:	n/a	chr22:30634865-30634874
6	POLR2A	chr22:30634489-30636429	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr22:30631062-30645095	IMR90	lung:	n/a	n/a
8	ELF1	chr22:30634481-30635078	A549	lung:	n/a	n/a
9	SIN3AK20	chr22:30634442-30635021	A549	lung:	n/a	n/a
10	TCF7L2	chr22:30634741-30635132	PANC-1	pancreas:	n/a	chr22:30634889-30634903
11	MAZ	chr22:30633617-30643724	IMR90	lung:	n/a	chr22:30642443-30642453 chr22:30641422-30641431 chr22:30642906-30642916 chr22:30634865-30634874 chr22:30640700-30640710
12	POLR2A	chr22:30634679-30636374	MCF-7	breast:	n/a	n/a
13	POLR2A	chr22:30633461-30651267	A549	lung:	n/a	n/a
14	BCL3	chr22:30633305-30635929	A549	lung:	n/a	chr22:30634361-30634374 chr22:30634377-30634386 chr22:30635486-30635499
15	KAP1	chr22:30634555-30635058	U2OS	brain:	n/a	n/a
16	CHD1	chr22:30633082-30643695	IMR90	lung:	n/a	chr22:30642644-30642654
17	JUND	chr22:30634383-30635140	A549	lung:	n/a	n/a
18	POLR2A	chr22:30634612-30635984	U87	brain:	n/a	n/a
19	TCF12	chr22:30634366-30636109	A549	lung:	n/a	n/a
20	SP1	chr22:30634473-30635156	A549	lung:	n/a	n/a
21	PBX3	chr22:30634538-30635827	A549	lung:	n/a	n/a
22	BCL3	chr22:30634374-30635662	A549	lung:	n/a	chr22:30634377-30634386 chr22:30635486-30635499
23	POLR2A	chr22:30634569-30636382	U87	brain:	n/a	n/a
24	POLR2A	chr22:30634712-30635271	A549	lung:	n/a	n/a
25	ZNF263	chr22:30634506-30634944	HEK293-T-REx	kidney:	n/a	chr22:30634712-30634733 chr22:30634684-30634693
26	GATA3	chr22:30634402-30635315	A549	lung:	n/a	n/a
27	EP300	chr22:30634466-30635743	A549	lung:	n/a	n/a
28	E2F6	chr22:30634625-30634952	A549	lung:	n/a	chr22:30634765-30634777
29	POLR2A	chr22:30634624-30635243	A549	lung:	n/a	n/a
30	SP1	chr22:30634508-30635168	A549	lung:	n/a	n/a
31	TCF12	chr22:30634553-30635000	A549	lung:	n/a	n/a
32	MAX	chr22:30634484-30635986	A549	lung:	n/a	chr22:30634865-30634874
33	POLR2A	chr22:30634404-30635881	HCT-116	colon:	n/a	n/a
34	POLR2A	chr22:30634469-30646541	HCT-116	colon:	n/a	n/a
35	PBX3	chr22:30634208-30635824	A549	lung:	n/a	n/a
36	EP300	chr22:30634496-30635413	A549	lung:	n/a	n/a
37	E2F6	chr22:30634126-30635368	A549	lung:	n/a	chr22:30634765-30634777
38	POLR2A	chr22:30634647-30635119	ECC-1	luminal epithelium:	n/a	n/a
39	YY1	chr22:30634681-30635230	A549	lung:	n/a	chr22:30635041-30635049

Variant related genes	Relation type
ENSG00000232530	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12166309	1.00[EUR][1000 genomes]
rs12169153	1.00[EUR][1000 genomes]
rs16988421	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56897799	1.00[EUR][1000 genomes]
rs5997599	1.00[EUR][1000 genomes]
rs6006413	1.00[EUR][1000 genomes]
rs6006417	1.00[EUR][1000 genomes]
rs60836642	1.00[EUR][1000 genomes]
rs61732271	1.00[EUR][1000 genomes]
rs7286437	1.00[EUR][1000 genomes]
rs7291157	1.00[EUR][1000 genomes]
rs73404536	1.00[AMR][1000 genomes]
rs73404556	1.00[EUR][1000 genomes]
rs73881424	1.00[EUR][1000 genomes]
rs73883356	1.00[EUR][1000 genomes]
rs8142884	1.00[EUR][1000 genomes]
rs9620975	1.00[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	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv914969	chr22:30619599-30691631	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30625200-30637000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr22:30630800-30635000	Enhancers	Placenta	Placenta
3	chr22:30630800-30635600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:30630800-30636600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:30631400-30637400	Weak transcription	Fetal Brain Male	brain
6	chr22:30631400-30639800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:30631400-30641600	Weak transcription	Right Atrium	heart
8	chr22:30631600-30635000	Weak transcription	Esophagus	oesophagus
9	chr22:30631600-30636400	Enhancers	HSMM	muscle
10	chr22:30631800-30635000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr22:30631800-30639400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr22:30632000-30636600	Weak transcription	Colonic Mucosa	Colon
13	chr22:30632000-30638600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr22:30632000-30641400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr22:30632400-30638600	Weak transcription	Spleen	Spleen
16	chr22:30632400-30639600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr22:30632400-30640800	Weak transcription	Lung	lung
18	chr22:30632600-30639400	Weak transcription	NHDF-Ad	bronchial
19	chr22:30632600-30641000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr22:30632600-30641400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr22:30632600-30645200	Weak transcription	Hela-S3	cervix
22	chr22:30632800-30637000	Weak transcription	HMEC	breast
23	chr22:30633000-30635000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr22:30633000-30635600	Weak transcription	Osteobl	bone
25	chr22:30633000-30636800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr22:30633400-30635600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr22:30633400-30636000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr22:30633600-30635000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr22:30633600-30635200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr22:30633600-30637200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr22:30633600-30638400	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr22:30633800-30635000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr22:30633800-30635200	Enhancers	H1 Cell Line	embryonic stem cell
34	chr22:30633800-30635600	Enhancers	Fetal Intestine Large	intestine
35	chr22:30633800-30635800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr22:30633800-30640200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr22:30634000-30635200	Enhancers	Fetal Intestine Small	intestine
38	chr22:30634000-30635200	Enhancers	Placenta Amnion	Placenta Amnion
39	chr22:30634000-30635800	Enhancers	Ovary	ovary
40	chr22:30634000-30636600	Enhancers	Fetal Stomach	stomach
41	chr22:30634000-30637600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr22:30634000-30638400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr22:30634000-30640400	Weak transcription	Dnd41	blood
44	chr22:30634000-30646800	Genic enhancers	A549	lung
45	chr22:30634200-30635000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr22:30634200-30635400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr22:30634200-30636000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr22:30634400-30635000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:30634400-30635000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr22:30634400-30635000	Enhancers	Fetal Thymus	thymus

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