Variant report

Variant	rs28372773
Chromosome Location	chr22:28315268-28315269
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	TAF1	chr22:28314987-28316393	H1-hESC	embryonic stem cell:	n/a	n/a
2	RELA	chr22:28314410-28315735	GM19099	blood:	n/a	n/a
3	MXI1	chr22:28314297-28316314	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr22:28314286-28316127	GM12891	blood:	n/a	n/a
5	TBP	chr22:28315018-28316379	GM12878	blood:	n/a	n/a
6	POLR2A	chr22:28314871-28316467	GM12878	blood:	n/a	n/a
7	CREB1	chr22:28314996-28315719	HepG2	liver:	n/a	n/a
8	MAFK	chr22:28315217-28315545	HepG2	liver:	n/a	n/a
9	SMC3	chr22:28315229-28315754	Hela-S3	cervix:	n/a	n/a
10	BRCA1	chr22:28315205-28315743	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr22:28314826-28316650	HUVEC	blood vessel:	n/a	n/a
12	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
13	CEBPB	chr22:28315233-28315594	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr22:28314805-28316269	PFSK-1	brain:	n/a	n/a
15	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
16	MXI1	chr22:28314293-28316147	HepG2	liver:	n/a	n/a
17	MAX	chr22:28315038-28316066	MCF-7	breast:	n/a	n/a
18	POLR2A	chr22:28314460-28316375	Hela-S3	cervix:	n/a	n/a
19	E2F4	chr22:28315199-28315735	MCF10A-Er-Src	breast:	n/a	chr22:28315258-28315267 chr22:28315246-28315255 chr22:28315289-28315298
20	JUN	chr22:28315147-28315617	K562	blood:	n/a	chr22:28315267-28315276 chr22:28315259-28315268
21	MYC	chr22:28315241-28315538	MCF-7	breast:	n/a	n/a
22	JUND	chr22:28315145-28315815	K562	blood:	n/a	chr22:28315267-28315276 chr22:28315259-28315268
23	MAX	chr22:28315183-28315802	K562	blood:	n/a	n/a
24	RCOR1	chr22:28315162-28316403	K562	blood:	n/a	n/a
25	POLR2A	chr22:28314924-28316380	Hela-S3	cervix:	n/a	n/a
26	CHD2	chr22:28314389-28316322	GM12878	blood:	n/a	n/a
27	POLR2A	chr22:28314980-28315807	K562	blood:	n/a	n/a
28	POLR2A	chr22:28314996-28315849	U87	brain:	n/a	n/a
29	POLR2A	chr22:28314608-28315953	K562	blood:	n/a	n/a
30	SIN3A	chr22:28314004-28316383	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr22:28314272-28316270	GM19193	blood:	n/a	n/a
32	CREB1	chr22:28314909-28316088	HepG2	liver:	n/a	n/a
33	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
34	EBF1	chr22:28315250-28316126	GM12878	blood:	n/a	n/a
35	POLR2A	chr22:28315009-28315753	PANC-1	pancreas:	n/a	n/a
36	HCFC1	chr22:28314278-28316374	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr22:28314467-28316052	GM12878	blood:	n/a	n/a
38	MAFK	chr22:28315144-28315885	Hela-S3	cervix:	n/a	n/a
39	ZKSCAN1	chr22:28315212-28316208	Hela-S3	cervix:	n/a	n/a
40	USF1	chr22:28315172-28315563	SK-N-SH_RA	brain:	n/a	n/a
41	POLR2A	chr22:28314498-28316356	H1-neurons	neurons:	n/a	n/a
42	CREB1	chr22:28314944-28315761	H1-hESC	embryonic stem cell:	n/a	n/a
43	NFYB	chr22:28315241-28315497	Hela-S3	cervix:	n/a	n/a
44	MYC	chr22:28314597-28315544	H1-hESC	embryonic stem cell:	n/a	chr22:28315026-28315036 chr22:28314905-28314914
45	POLR2A	chr22:28314592-28315768	K562	blood:	n/a	n/a
46	BHLHE40	chr22:28315214-28316080	K562	blood:	n/a	n/a
47	YY1	chr22:28315165-28315550	HCT-116	colon:	n/a	chr22:28315250-28315261
48	TBL1XR1	chr22:28315120-28315720	GM12878	blood:	n/a	n/a
49	HEY1	chr22:28315045-28315817	HepG2	liver:	n/a	n/a
50	TAF1	chr22:28314939-28316206	H1-neurons	neurons:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:28315223-28315273	HIPEpiC	eye:	n/a
2	chr22:28315223-28315273	HMEC	breast:	n/a
3	chr22:28315223-28315273	HCPEpiC	choroid plexus:	n/a
4	chr22:28315223-28315273	AG04449	skin:	fetal
5	chr22:28315223-28315273	ECC-1	luminal epithelium:	n/a
6	chr22:28315223-28315273	AG10803	skin:	n/a
7	chr22:28315223-28315273	Hepatocyte	liver:	n/a
8	chr22:28315223-28315273	SKMC	muscle:	n/a
9	chr22:28315223-28315273	HCF	heart:	n/a
10	chr22:28315223-28315273	HepG2	liver:	n/a
11	chr22:28315223-28315273	NT2-D1	testis:	n/a
12	chr22:28315223-28315273	HRE	kidney:	n/a
13	chr22:28315223-28315273	RPTEC	kidney:	n/a
14	chr22:28315223-28315273	SK-N-SH	brain:	n/a
15	chr22:28315223-28315273	GM12892	blood:	n/a
16	chr22:28315223-28315273	H1-hESC	embryonic stem cell:	embryo
17	chr22:28315223-28315273	T-47D	breast:	n/a
18	chr22:28315223-28315273	ovcar-3	ovarian:	n/a
19	chr22:28315223-28315273	IMR90	lung:	fetal
20	chr22:28315223-28315273	HEK293	kidney:	embryo
21	chr22:28315223-28315273	AG04450	lung:	fetal
22	chr22:28315223-28315273	GM19239	blood:	n/a
23	chr22:28315223-28315273	BE2_C	brain:	n/a
24	chr22:28315223-28315273	MCF10A-Er-Src	breast:	n/a
25	chr22:28315223-28315273	HCT-116	colon:	n/a
26	chr22:28315223-28315273	GM12878	blood:	n/a
27	chr22:28315223-28315273	HNPCEpiC	eye:	n/a
28	chr22:28315223-28315273	SK-N-MC	brain:	n/a
29	chr22:28315223-28315273	HUVEC	blood vessel:	n/a
30	chr22:28315223-28315273	NB4	blood:	n/a
31	chr22:28315223-28315273	LNCaP	prostate:	n/a
32	chr22:28315223-28315273	PANC-1	pancreas:	n/a
33	chr22:28315223-28315273	GM06990	blood:	n/a
34	chr22:28315223-28315273	HRPEpiC	eye:	n/a
35	chr22:28315223-28315273	PFSK-1	brain:	n/a
36	chr22:28315223-28315273	U87	brain:	n/a
37	chr22:28315223-28315273	A549	lung:	n/a
38	chr22:28315223-28315273	HEEpiC	esophagus:	n/a
39	chr22:28315223-28315273	K562	blood:	n/a
40	chr22:28315223-28315273	BJ	skin:	n/a
41	chr22:28315223-28315273	NH-A	brain:	n/a
42	chr22:28315223-28315273	ProgFib	skin:	n/a
43	chr22:28315223-28315273	AG09319	gingival:	n/a
44	chr22:28315223-28315273	HCM	heart:	n/a
45	chr22:28315223-28315273	AG09309	skin:	n/a
46	chr22:28315223-28315273	AoSMC	blood vessel:	n/a
47	chr22:28315223-28315273	NHDF-neo	bronchial:	n/a
48	chr22:28315223-28315273	GM12891	blood:	n/a
49	chr22:28315223-28315273	SAEC	small airway:	n/a
50	chr22:28315223-28315273	Caco-2	colon:	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
PITPNB	TF binding region
PITPNB	CpG island
TTC28-AS1	CpG island
ENSG00000235954	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000149932	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12160891	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2143180	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2267125	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2345019	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752651	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5752670	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5762395	0.82[ASN][1000 genomes]
rs5762396	0.82[ASN][1000 genomes]
rs5762398	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5762400	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs5762404	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5762410	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762412	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762425	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5762428	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5997318	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6005674	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714743	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73166732	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[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	chr22:28313800-28316200	Active TSS	Lung	lung
7	chr22:28313800-28316400	Active TSS	Left Ventricle	heart
8	chr22:28313800-28316600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr22:28314000-28315800	Active TSS	Fetal Muscle Trunk	muscle
10	chr22:28314000-28316200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr22:28314000-28316400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr22:28314000-28316400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr22:28314000-28316400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr22:28314200-28315400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr22:28314200-28315600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr22:28314200-28315600	Active TSS	HMEC	breast
17	chr22:28314200-28315600	Active TSS	NH-A	brain
18	chr22:28314200-28315600	Active TSS	NHLF	lung
19	chr22:28314200-28315800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr22:28314200-28315800	Active TSS	Colonic Mucosa	Colon
21	chr22:28314200-28315800	Active TSS	Pancreas	Pancrea
22	chr22:28314200-28315800	Active TSS	HSMMtube	muscle
23	chr22:28314200-28315800	Active TSS	NHDF-Ad	bronchial
24	chr22:28314200-28316000	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr22:28314200-28316000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr22:28314200-28316000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr22:28314200-28316000	Active TSS	Brain Hippocampus Middle	brain
28	chr22:28314200-28316000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr22:28314200-28316000	Active TSS	Fetal Heart	heart
30	chr22:28314200-28316000	Active TSS	Fetal Kidney	kidney
31	chr22:28314200-28316000	Active TSS	Placenta Amnion	Placenta Amnion
32	chr22:28314200-28316200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr22:28314200-28316200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr22:28314200-28316200	Active TSS	Brain Germinal Matrix	brain
35	chr22:28314200-28316200	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr22:28314200-28316200	Active TSS	HSMM	muscle
37	chr22:28314200-28316400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr22:28314200-28316400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr22:28314200-28316400	Active TSS	H9 Cell Line	embryonic stem cell
40	chr22:28314200-28316400	Active TSS	Right Ventricle	heart
41	chr22:28314200-28316600	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr22:28314200-28316600	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr22:28314200-28316600	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr22:28314200-28316600	Active TSS	Right Atrium	heart
45	chr22:28314200-28316600	Active TSS	Hela-S3	cervix
46	chr22:28314200-28316800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr22:28314200-28316800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr22:28314200-28316800	Active TSS	Psoas Muscle	Psoas
49	chr22:28314200-28316800	Active TSS	Rectal Smooth Muscle	rectum
50	chr22:28314200-28316800	Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links