Variant report

Variant	rs16986969
Chromosome Location	chr22:28314902-28314903
allele	C/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	RELA	chr22:28314410-28315735	GM19099	blood:	n/a	n/a
2	MXI1	chr22:28314297-28316314	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr22:28314286-28316127	GM12891	blood:	n/a	n/a
4	POLR2A	chr22:28314443-28315004	GM12891	blood:	n/a	n/a
5	POLR2A	chr22:28314844-28315009	A549	lung:	n/a	n/a
6	POLR2A	chr22:28314871-28316467	GM12878	blood:	n/a	n/a
7	POLR2A	chr22:28314826-28316650	HUVEC	blood vessel:	n/a	n/a
8	MAX	chr22:28314186-28316063	ECC-1	luminal epithelium:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
9	POLR2A	chr22:28314805-28316269	PFSK-1	brain:	n/a	n/a
10	MAX	chr22:28314263-28315900	A549	lung:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
11	MXI1	chr22:28314293-28316147	HepG2	liver:	n/a	n/a
12	UBTF	chr22:28314500-28315056	K562	blood:	n/a	n/a
13	POLR2A	chr22:28314460-28316375	Hela-S3	cervix:	n/a	n/a
14	CHD2	chr22:28314389-28316322	GM12878	blood:	n/a	n/a
15	POLR2A	chr22:28314608-28315953	K562	blood:	n/a	n/a
16	SIN3A	chr22:28314004-28316383	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr22:28314272-28316270	GM19193	blood:	n/a	n/a
18	MYC	chr22:28314311-28315731	K562	blood:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
19	HCFC1	chr22:28314278-28316374	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr22:28314467-28316052	GM12878	blood:	n/a	n/a
21	POLR2A	chr22:28314498-28316356	H1-neurons	neurons:	n/a	n/a
22	SIN3AK20	chr22:28314186-28315234	K562	blood:	n/a	n/a
23	MYC	chr22:28314597-28315544	H1-hESC	embryonic stem cell:	n/a	chr22:28315026-28315036 chr22:28314905-28314914
24	POLR2A	chr22:28314592-28315768	K562	blood:	n/a	n/a
25	MYC	chr22:28314874-28314930	K562	blood:	n/a	chr22:28314905-28314914
26	POLR2A	chr22:28314760-28315760	K562	blood:	n/a	n/a
27	POLR2A	chr22:28314860-28315958	HL-60	blood:	n/a	n/a
28	POLR2A	chr22:28314617-28315848	Gliobla	brain:	n/a	n/a
29	MAX	chr22:28314293-28315941	SK-N-SH	brain:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
30	MAX	chr22:28314145-28316178	GM12878	blood:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
31	POLR2A	chr22:28314861-28315776	GM12878	blood:	n/a	n/a
32	POLR2A	chr22:28314737-28316509	PFSK-1	brain:	n/a	n/a
33	SIN3AK20	chr22:28314832-28315129	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr22:28314185-28316416	A549	lung:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
35	MYC	chr22:28314309-28316364	MCF10A-Er-Src	breast:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
36	RELA	chr22:28314398-28316534	GM10847	blood:	n/a	n/a
37	MAX	chr22:28314257-28315971	K562	blood:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
38	ZBTB7A	chr22:28314615-28315406	ECC-1	luminal epithelium:	n/a	chr22:28315031-28315040
39	POLR2A	chr22:28314347-28316440	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr22:28314766-28315733	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr22:28314372-28315876	MCF-7	breast:	n/a	n/a
42	MAX	chr22:28314301-28316075	NB4	blood:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
43	POLR2A	chr22:28314411-28316340	GM19099	blood:	n/a	n/a
44	POLR2A	chr22:28314385-28316390	HepG2	liver:	n/a	n/a
45	MYC	chr22:28314242-28315818	A549	lung:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
46	RUNX3	chr22:28314462-28314968	GM12878	blood:	n/a	n/a
47	POLR2A	chr22:28314180-28316964	IMR90	lung:	n/a	n/a
48	POLR2A	chr22:28314582-28315007	HUVEC	blood vessel:	n/a	n/a
49	MYC	chr22:28314753-28315023	HepG2	liver:	n/a	chr22:28314905-28314914
50	POLR2A	chr22:28314390-28316285	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:28314414..28316359-chr22:28329725..28332798,3	MCF-7	breast:
2	chr22:28314687..28317374-chr22:28386537..28389209,3	MCF-7	breast:
3	chr22:28314744..28315373-chr6:27114490..27115193,2	Hela-S3	cervix:
4	chr16:29973010..29973800-chr22:28314779..28315664,2	NB4	blood:

Variant related genes	Relation type
TTC28-AS1	TF binding region
ENSG00000149932	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000235954	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12053760	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2142561	0.97[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2143181	0.83[ASN][1000 genomes]
rs2235574	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2294820	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs5752658	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5752663	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5752671	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5752672	0.98[EUR][1000 genomes]
rs5762408	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs5762419	1.00[EUR][1000 genomes]
rs5762422	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5762424	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 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	chr22:28311200-28316200	Active TSS	GM12878-XiMat	blood
2	chr22:28313000-28317200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr22:28313200-28316200	Active TSS	Aorta	Aorta
4	chr22:28313600-28315400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr22:28313600-28316200	Active TSS	Ovary	ovary
6	chr22:28313800-28315200	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr22:28313800-28316200	Active TSS	Lung	lung
8	chr22:28313800-28316400	Active TSS	Left Ventricle	heart
9	chr22:28313800-28316600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr22:28314000-28315800	Active TSS	Fetal Muscle Trunk	muscle
11	chr22:28314000-28316200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr22:28314000-28316400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr22:28314000-28316400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr22:28314000-28316400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr22:28314200-28315200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr22:28314200-28315200	ZNF genes & repeats	Fetal Brain Male	brain
17	chr22:28314200-28315400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr22:28314200-28315600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr22:28314200-28315600	Active TSS	HMEC	breast
20	chr22:28314200-28315600	Active TSS	NH-A	brain
21	chr22:28314200-28315600	Active TSS	NHLF	lung
22	chr22:28314200-28315800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr22:28314200-28315800	Active TSS	Colonic Mucosa	Colon
24	chr22:28314200-28315800	Active TSS	Pancreas	Pancrea
25	chr22:28314200-28315800	Active TSS	HSMMtube	muscle
26	chr22:28314200-28315800	Active TSS	NHDF-Ad	bronchial
27	chr22:28314200-28316000	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr22:28314200-28316000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
29	chr22:28314200-28316000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr22:28314200-28316000	Active TSS	Brain Hippocampus Middle	brain
31	chr22:28314200-28316000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr22:28314200-28316000	Active TSS	Fetal Heart	heart
33	chr22:28314200-28316000	Active TSS	Fetal Kidney	kidney
34	chr22:28314200-28316000	Active TSS	Placenta Amnion	Placenta Amnion
35	chr22:28314200-28316200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr22:28314200-28316200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr22:28314200-28316200	Active TSS	Brain Germinal Matrix	brain
38	chr22:28314200-28316200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr22:28314200-28316200	Active TSS	HSMM	muscle
40	chr22:28314200-28316400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr22:28314200-28316400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr22:28314200-28316400	Active TSS	H9 Cell Line	embryonic stem cell
43	chr22:28314200-28316400	Active TSS	Right Ventricle	heart
44	chr22:28314200-28316600	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr22:28314200-28316600	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr22:28314200-28316600	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr22:28314200-28316600	Active TSS	Right Atrium	heart
48	chr22:28314200-28316600	Active TSS	Hela-S3	cervix
49	chr22:28314200-28316800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:28314200-28316800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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