Variant report

Variant	rs16985722
Chromosome Location	chr22:28315465-28315466
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	GTF2B	chr22:28315414-28315685	K562	blood:	n/a	n/a
2	POLR2A	chr22:28315353-28315805	HUVEC	blood vessel:	n/a	n/a
3	TAF1	chr22:28314987-28316393	H1-hESC	embryonic stem cell:	n/a	n/a
4	RELA	chr22:28314410-28315735	GM19099	blood:	n/a	n/a
5	MXI1	chr22:28314297-28316314	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr22:28314286-28316127	GM12891	blood:	n/a	n/a
7	TBP	chr22:28315018-28316379	GM12878	blood:	n/a	n/a
8	POLR2A	chr22:28314871-28316467	GM12878	blood:	n/a	n/a
9	CREB1	chr22:28314996-28315719	HepG2	liver:	n/a	n/a
10	MAFK	chr22:28315217-28315545	HepG2	liver:	n/a	n/a
11	SMC3	chr22:28315229-28315754	Hela-S3	cervix:	n/a	n/a
12	BRCA1	chr22:28315205-28315743	Hela-S3	cervix:	n/a	n/a
13	EGR1	chr22:28315426-28315629	GM12878	blood:	n/a	n/a
14	ATF3	chr22:28315275-28315662	A549	lung:	n/a	n/a
15	POLR2A	chr22:28314826-28316650	HUVEC	blood vessel:	n/a	n/a
16	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
17	ZNF263	chr22:28315291-28316402	HEK293-T-REx	kidney:	n/a	n/a
18	CEBPB	chr22:28315233-28315594	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr22:28314805-28316269	PFSK-1	brain:	n/a	n/a
20	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
21	MXI1	chr22:28314293-28316147	HepG2	liver:	n/a	n/a
22	MAX	chr22:28315038-28316066	MCF-7	breast:	n/a	n/a
23	POLR2A	chr22:28314460-28316375	Hela-S3	cervix:	n/a	n/a
24	E2F4	chr22:28315199-28315735	MCF10A-Er-Src	breast:	n/a	chr22:28315258-28315267 chr22:28315246-28315255 chr22:28315289-28315298
25	JUN	chr22:28315147-28315617	K562	blood:	n/a	chr22:28315267-28315276 chr22:28315259-28315268
26	MYC	chr22:28315241-28315538	MCF-7	breast:	n/a	n/a
27	JUND	chr22:28315145-28315815	K562	blood:	n/a	chr22:28315267-28315276 chr22:28315259-28315268
28	MAX	chr22:28315183-28315802	K562	blood:	n/a	n/a
29	RCOR1	chr22:28315162-28316403	K562	blood:	n/a	n/a
30	POLR2A	chr22:28314924-28316380	Hela-S3	cervix:	n/a	n/a
31	CHD2	chr22:28314389-28316322	GM12878	blood:	n/a	n/a
32	POLR2A	chr22:28314980-28315807	K562	blood:	n/a	n/a
33	POLR2A	chr22:28314996-28315849	U87	brain:	n/a	n/a
34	POLR2A	chr22:28314608-28315953	K562	blood:	n/a	n/a
35	SIN3A	chr22:28314004-28316383	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr22:28314272-28316270	GM19193	blood:	n/a	n/a
37	CREB1	chr22:28314909-28316088	HepG2	liver:	n/a	n/a
38	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
39	EBF1	chr22:28315250-28316126	GM12878	blood:	n/a	n/a
40	POLR2A	chr22:28315009-28315753	PANC-1	pancreas:	n/a	n/a
41	TAF1	chr22:28315409-28316001	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr22:28315353-28316058	GM12891	blood:	n/a	n/a
43	HCFC1	chr22:28314278-28316374	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr22:28314467-28316052	GM12878	blood:	n/a	n/a
45	CEBPB	chr22:28315345-28315517	K562	blood:	n/a	n/a
46	FOS	chr22:28315338-28315673	MCF10A-Er-Src	breast:	n/a	n/a
47	MAFK	chr22:28315144-28315885	Hela-S3	cervix:	n/a	n/a
48	TFAP2A	chr22:28315280-28316262	Hela-S3	cervix:	n/a	n/a
49	ZKSCAN1	chr22:28315212-28316208	Hela-S3	cervix:	n/a	n/a
50	USF1	chr22:28315172-28315563	SK-N-SH_RA	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:28315424-28315474	PrEC	prostate:	n/a
2	chr22:28315424-28315474	GM12892	blood:	n/a
3	chr22:28315424-28315474	H1-hESC	embryonic stem cell:	embryo
4	chr22:28315424-28315474	K562	blood:	n/a
5	chr22:28315424-28315474	BE2_C	brain:	n/a
6	chr22:28315424-28315474	NHDF-neo	bronchial:	n/a
7	chr22:28315424-28315474	Hepatocyte	liver:	n/a
8	chr22:28315424-28315474	AG10803	skin:	n/a
9	chr22:28315424-28315474	T-47D	breast:	n/a
10	chr22:28315424-28315474	GM12878	blood:	n/a
11	chr22:28315424-28315474	HNPCEpiC	eye:	n/a
12	chr22:28315424-28315474	A549	lung:	n/a
13	chr22:28315424-28315474	AoSMC	blood vessel:	n/a
14	chr22:28315424-28315474	NHBE	bronchial:	n/a
15	chr22:28315424-28315474	HCF	heart:	n/a
16	chr22:28315424-28315474	ECC-1	luminal epithelium:	n/a
17	chr22:28315424-28315474	Caco-2	colon:	n/a
18	chr22:28315424-28315474	HRPEpiC	eye:	n/a
19	chr22:28315424-28315474	MCF-7	breast:	n/a
20	chr22:28315424-28315474	GM19239	blood:	n/a
21	chr22:28315424-28315474	HMEC	breast:	n/a
22	chr22:28315424-28315474	SK-N-SH	brain:	n/a
23	chr22:28315424-28315474	SAEC	small airway:	n/a
24	chr22:28315424-28315474	HEEpiC	esophagus:	n/a
25	chr22:28315424-28315474	HPAEpiC	pulmonary alveolar:	n/a
26	chr22:28315424-28315474	SK-N-MC	brain:	n/a
27	chr22:28315424-28315474	SKMC	muscle:	n/a
28	chr22:28315424-28315474	NT2-D1	testis:	n/a
29	chr22:28315424-28315474	GM12891	blood:	n/a
30	chr22:28315424-28315474	AG04450	lung:	fetal
31	chr22:28315424-28315474	LNCaP	prostate:	n/a
32	chr22:28315424-28315474	HepG2	liver:	n/a
33	chr22:28315424-28315474	U87	brain:	n/a
34	chr22:28315424-28315474	AG09319	gingival:	n/a
35	chr22:28315424-28315474	BJ	skin:	n/a
36	chr22:28315424-28315474	PFSK-1	brain:	n/a
37	chr22:28315424-28315474	HIPEpiC	eye:	n/a
38	chr22:28315424-28315474	AG09309	skin:	n/a
39	chr22:28315424-28315474	ovcar-3	ovarian:	n/a
40	chr22:28315424-28315474	PANC-1	pancreas:	n/a
41	chr22:28315424-28315474	GM06990	blood:	n/a
42	chr22:28315424-28315474	HRE	kidney:	n/a
43	chr22:28315424-28315474	HCT-116	colon:	n/a
44	chr22:28315424-28315474	HUVEC	blood vessel:	n/a
45	chr22:28315424-28315474	Hela-S3	cervix:	n/a
46	chr22:28315424-28315474	HRCEpiC	kidney:	n/a
47	chr22:28315424-28315474	SK-N-SH_RA	brain:	n/a
48	chr22:28315424-28315474	HCPEpiC	choroid plexus:	n/a
49	chr22:28315424-28315474	NH-A	brain:	n/a
50	chr22:28315424-28315474	MCF10A-Er-Src	breast:	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	chr16:29973010..29973800-chr22:28314779..28315664,2	NB4	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSCB-1	chr22:28315445-28315533	ENSG00000235954
2	lnc-HSCB-1	chr22:28315417-28315533	ENSG00000235954
3	lnc-HSCB-1	chr22:28315425-28315533	ENSG00000235954
4	lnc-HSCB-1	chr22:28315445-28315533	ENSG00000235954
5	lnc-HSCB-1	chr22:28315389-28315533	ENSG00000235954
6	lnc-HSCB-1	chr22:28315458-28315533	ENSG00000235954
7	lnc-HSCB-1	chr22:28315460-28315954	ENSG00000235954
8	lnc-HSCB-1	chr22:28315380-28315533	ENSG00000235954
9	lnc-HSCB-1	chr22:28315428-28315533	ENSG00000235954
10	lnc-HSCB-1	chr22:28315364-28315533	ENSG00000235954
11	lnc-HSCB-1	chr22:28315445-28315533	ENSG00000235954
12	lnc-HSCB-1	chr22:28315364-28315533	NONHSAT084607
13	lnc-HSCB-1	chr22:28315356-28315533	NONHSAT084606

Variant related genes	Relation type
TTC28-AS1	TF binding region
PITPNB	TF binding region
TTC28-AS1	CpG island
PITPNB	CpG island
ENSG00000235954	Chromatin interaction
ENSG00000149932	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1016495	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12483793	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12484349	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17484428	1.00[CEU][hapmap]
rs1807581	0.98[ASN][1000 genomes]
rs2076505	1.00[CEU][hapmap]
rs2235713	1.00[CEU][hapmap]
rs2267127	0.98[ASN][1000 genomes]
rs2267128	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294818	1.00[CEU][hapmap]
rs28529300	0.98[ASN][1000 genomes]
rs56156048	0.98[ASN][1000 genomes]
rs7292046	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs738454	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8138623	1.00[CEU][hapmap]
rs9613545	0.80[ASN][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	chr22:28313600-28316200	Active TSS	Ovary	ovary
5	chr22:28313800-28316200	Active TSS	Lung	lung
6	chr22:28313800-28316400	Active TSS	Left Ventricle	heart
7	chr22:28313800-28316600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr22:28314000-28315800	Active TSS	Fetal Muscle Trunk	muscle
9	chr22:28314000-28316200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr22:28314000-28316400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr22:28314000-28316400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr22:28314000-28316400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr22:28314200-28315600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr22:28314200-28315600	Active TSS	HMEC	breast
15	chr22:28314200-28315600	Active TSS	NH-A	brain
16	chr22:28314200-28315600	Active TSS	NHLF	lung
17	chr22:28314200-28315800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr22:28314200-28315800	Active TSS	Colonic Mucosa	Colon
19	chr22:28314200-28315800	Active TSS	Pancreas	Pancrea
20	chr22:28314200-28315800	Active TSS	HSMMtube	muscle
21	chr22:28314200-28315800	Active TSS	NHDF-Ad	bronchial
22	chr22:28314200-28316000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr22:28314200-28316000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
24	chr22:28314200-28316000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr22:28314200-28316000	Active TSS	Brain Hippocampus Middle	brain
26	chr22:28314200-28316000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr22:28314200-28316000	Active TSS	Fetal Heart	heart
28	chr22:28314200-28316000	Active TSS	Fetal Kidney	kidney
29	chr22:28314200-28316000	Active TSS	Placenta Amnion	Placenta Amnion
30	chr22:28314200-28316200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr22:28314200-28316200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr22:28314200-28316200	Active TSS	Brain Germinal Matrix	brain
33	chr22:28314200-28316200	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr22:28314200-28316200	Active TSS	HSMM	muscle
35	chr22:28314200-28316400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr22:28314200-28316400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr22:28314200-28316400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr22:28314200-28316400	Active TSS	Right Ventricle	heart
39	chr22:28314200-28316600	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr22:28314200-28316600	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr22:28314200-28316600	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr22:28314200-28316600	Active TSS	Right Atrium	heart
43	chr22:28314200-28316600	Active TSS	Hela-S3	cervix
44	chr22:28314200-28316800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr22:28314200-28316800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr22:28314200-28316800	Active TSS	Psoas Muscle	Psoas
47	chr22:28314200-28316800	Active TSS	Rectal Smooth Muscle	rectum
48	chr22:28314200-28316800	Active TSS	A549	lung
49	chr22:28314200-28317200	Active TSS	K562	blood
50	chr22:28314400-28315600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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