Variant report

Variant	rs28384449
Chromosome Location	chr1:226070429-226070430
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	E2F6	chr1:226069714-226070614	K562	blood:	n/a	chr1:226070093-226070102 chr1:226070006-226070016
2	POLR2A	chr1:226069203-226071113	K562	blood:	n/a	n/a
3	MAX	chr1:226069749-226071155	A549	lung:	n/a	chr1:226070644-226070654
4	MAX	chr1:226069697-226071236	A549	lung:	n/a	chr1:226070644-226070654
5	CTCF	chr1:226070340-226070490	HA-sp	spinal cord:	n/a	n/a
6	POLR2A	chr1:226069502-226071069	Hela-S3	cervix:	n/a	n/a
7	TBL1XR1	chr1:226069185-226070577	K562	blood:	n/a	n/a
8	POLR2A	chr1:226069535-226070448	MCF-7	breast:	n/a	n/a
9	POLR2A	chr1:226069509-226070558	MCF-7	breast:	n/a	n/a
10	HCFC1	chr1:226069406-226070548	K562	blood:	n/a	n/a
11	POLR2A	chr1:226069583-226070609	ProgFib	skin:	n/a	n/a
12	MAX	chr1:226069844-226070494	GM12878	blood:	n/a	n/a
13	CHD2	chr1:226069384-226071033	K562	blood:	n/a	chr1:226070578-226070588
14	HA-E2F1	chr1:226069811-226071141	MCF-7	breast:	n/a	chr1:226070093-226070102 chr1:226070006-226070016 chr1:226070891-226070905
15	SRF	chr1:226069775-226070536	MCF-7	breast:	n/a	n/a
16	POLR2A	chr1:226069738-226070473	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr1:226069446-226070966	K562	blood:	n/a	n/a
18	ZBTB7A	chr1:226068784-226070952	K562	blood:	n/a	chr1:226070384-226070395
19	POLR2A	chr1:226069574-226070467	GM12878	blood:	n/a	n/a
20	E2F6	chr1:226069776-226071160	H1-hESC	embryonic stem cell:	n/a	chr1:226070093-226070102 chr1:226070006-226070016 chr1:226070891-226070905
21	POLR2A	chr1:226069835-226070446	HCT-116	colon:	n/a	n/a
22	STAT5A	chr1:226070102-226070514	GM12878	blood:	n/a	n/a
23	MYC	chr1:226069214-226071116	K562	blood:	n/a	chr1:226070644-226070654
24	STAT1	chr1:226070006-226070584	GM12878	blood:	n/a	n/a
25	GTF2F1	chr1:226070005-226070435	Hela-S3	cervix:	n/a	n/a
26	EGR1	chr1:226070230-226070814	K562	blood:	n/a	chr1:226070637-226070659 chr1:226070485-226070494 chr1:226070482-226070495 chr1:226070484-226070494 chr1:226070482-226070495 chr1:226070641-226070654 chr1:226070641-226070654 chr1:226070483-226070497 chr1:226070482-226070495 chr1:226070481-226070496 chr1:226070483-226070494 chr1:226070644-226070654 chr1:226070640-226070655
27	EP300	chr1:226070223-226070823	T-47D	breast:	n/a	chr1:226070229-226070245
28	ELF1	chr1:226070064-226070539	K562	blood:	n/a	chr1:226070143-226070152 chr1:226070357-226070366
29	TCF12	chr1:226069377-226071229	A549	lung:	n/a	chr1:226069792-226069800 chr1:226069933-226069940 chr1:226070523-226070530
30	POLR2A	chr1:226069774-226071015	ECC-1	luminal epithelium:	n/a	n/a
31	UBTF	chr1:226069313-226071120	K562	blood:	n/a	n/a
32	HEY1	chr1:226069718-226070455	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:226069459-226070950	GM18951	blood:	n/a	n/a
34	POLR2A	chr1:226069588-226070536	GM12891	blood:	n/a	n/a
35	E2F4	chr1:226069863-226071007	K562	blood:	n/a	chr1:226070093-226070102 chr1:226070006-226070016 chr1:226070891-226070905
36	TBP	chr1:226069979-226070969	H1-hESC	embryonic stem cell:	n/a	n/a
37	NFIC	chr1:226070399-226071149	ECC-1	luminal epithelium:	n/a	n/a
38	EGR1	chr1:226070106-226070747	H1-hESC	embryonic stem cell:	n/a	chr1:226070637-226070659 chr1:226070485-226070494 chr1:226070482-226070495 chr1:226070484-226070494 chr1:226070482-226070495 chr1:226070641-226070654 chr1:226070641-226070654 chr1:226070483-226070497 chr1:226070482-226070495 chr1:226070481-226070496 chr1:226070483-226070494 chr1:226070644-226070654 chr1:226070640-226070655
39	BACH1	chr1:226070382-226070566	K562	blood:	n/a	n/a
40	TFAP2C	chr1:226069164-226070942	Hela-S3	cervix:	n/a	chr1:226069573-226069588
41	ELF1	chr1:226069231-226070907	GM12878	blood:	n/a	chr1:226070008-226070017 chr1:226070143-226070152 chr1:226070357-226070366
42	JUND	chr1:226069257-226070584	K562	blood:	n/a	chr1:226069762-226069776 chr1:226070263-226070277
43	HEY1	chr1:226069239-226071026	K562	blood:	n/a	chr1:226070734-226070749
44	NR2F2	chr1:226068421-226070907	K562	blood:	n/a	n/a
45	POLR2A	chr1:226069239-226070667	PFSK-1	brain:	n/a	n/a
46	YY1	chr1:226070338-226070937	K562	blood:	n/a	chr1:226070581-226070592
47	POLR2A	chr1:226069773-226071162	SK-N-MC	brain:	n/a	n/a
48	MAX	chr1:226069715-226071146	ECC-1	luminal epithelium:	n/a	chr1:226070644-226070654
49	YY1	chr1:226069344-226071024	K562	blood:	n/a	chr1:226070008-226070017 chr1:226070006-226070017 chr1:226070143-226070152 chr1:226070581-226070592 chr1:226069490-226069499
50	HEY1	chr1:226069395-226070675	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:226070397-226070447	ovcar-3	ovarian:	n/a
2	chr1:226070397-226070447	AG04449	skin:	fetal
3	chr1:226070397-226070447	IMR90	lung:	fetal
4	chr1:226070397-226070447	SKMC	muscle:	n/a
5	chr1:226070397-226070447	HPAEpiC	pulmonary alveolar:	n/a
6	chr1:226070397-226070447	HRE	kidney:	n/a
7	chr1:226070397-226070447	SK-N-SH	brain:	n/a
8	chr1:226070397-226070447	SK-N-SH_RA	brain:	n/a
9	chr1:226070397-226070447	PrEC	prostate:	n/a
10	chr1:226070397-226070447	HCT-116	colon:	n/a
11	chr1:226070397-226070447	U87	brain:	n/a
12	chr1:226070397-226070447	HMEC	breast:	n/a
13	chr1:226070397-226070447	HCPEpiC	choroid plexus:	n/a
14	chr1:226070397-226070447	GM12878	blood:	n/a
15	chr1:226070397-226070447	HEK293	kidney:	embryo
16	chr1:226070397-226070447	SK-N-MC	brain:	n/a
17	chr1:226070397-226070447	AoSMC	blood vessel:	n/a
18	chr1:226070397-226070447	A549	lung:	n/a
19	chr1:226070397-226070447	GM12892	blood:	n/a
20	chr1:226070397-226070447	HUVEC	blood vessel:	n/a
21	chr1:226070397-226070447	HAEpiC	amniotic membrane:	n/a
22	chr1:226070397-226070447	HepG2	liver:	n/a
23	chr1:226070397-226070447	ProgFib	skin:	n/a
24	chr1:226070397-226070447	HEEpiC	esophagus:	n/a
25	chr1:226070397-226070447	HRPEpiC	eye:	n/a
26	chr1:226070397-226070447	K562	blood:	n/a
27	chr1:226070397-226070447	GM06990	blood:	n/a
28	chr1:226070397-226070447	RPTEC	kidney:	n/a
29	chr1:226070397-226070447	HNPCEpiC	eye:	n/a
30	chr1:226070397-226070447	NH-A	brain:	n/a
31	chr1:226070397-226070447	PFSK-1	brain:	n/a
32	chr1:226070397-226070447	NB4	blood:	n/a
33	chr1:226070397-226070447	NHDF-neo	bronchial:	n/a
34	chr1:226070397-226070447	AG04450	lung:	fetal
35	chr1:226070397-226070447	NT2-D1	testis:	n/a
36	chr1:226070397-226070447	MCF10A-Er-Src	breast:	n/a
37	chr1:226070397-226070447	Hepatocyte	liver:	n/a
38	chr1:226070397-226070447	Caco-2	colon:	n/a
39	chr1:226070397-226070447	SAEC	small airway:	n/a
40	chr1:226070397-226070447	HIPEpiC	eye:	n/a
41	chr1:226070397-226070447	BE2_C	brain:	n/a
42	chr1:226070397-226070447	Jurkat	blood:	n/a
43	chr1:226070397-226070447	H1-hESC	embryonic stem cell:	embryo
44	chr1:226070397-226070447	AG09309	skin:	n/a
45	chr1:226070397-226070447	Hela-S3	cervix:	n/a
46	chr1:226070397-226070447	HCF	heart:	n/a
47	chr1:226070397-226070447	NHBE	bronchial:	n/a
48	chr1:226070397-226070447	HCM	heart:	n/a
49	chr1:226070397-226070447	ECC-1	luminal epithelium:	n/a
50	chr1:226070397-226070447	HRCEpiC	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226070093..226070593-chr9:140168206..140168750,2	NB4	blood:
2	chr1:226053217..226056086-chr1:226069002..226071584,2	MCF-7	breast:
3	chr1:226068960..226071215-chr11:62609040..62611080,2	MCF-7	breast:
4	chr1:225964533..225968744-chr1:226068261..226071590,3	MCF-7	breast:
5	chr1:226070080..226072229-chr1:226145455..226147029,2	K562	blood:
6	chr1:226070069..226070803-chr1:226098754..226099255,2	MCF-7	breast:
7	chr1:226032510..226034899-chr1:226069383..226071490,2	MCF-7	breast:
8	chr1:226053727..226055880-chr1:226069290..226070897,2	MCF-7	breast:
9	chr1:226068530..226073051-chr1:226075073..226079547,5	MCF-7	breast:
10	chr1:226069198..226071720-chr1:226149361..226151916,2	MCF-7	breast:
11	chr1:226070277..226070992-chr15:45926572..45927323,2	Hela-S3	cervix:
12	chr1:226047047..226048850-chr1:226067848..226071913,3	MCF-7	breast:
13	chr1:226070165..226072280-chr1:226086600..226088627,2	K562	blood:
14	chr1:226067837..226071624-chr1:226184531..226189088,6	K562	blood:
15	chr1:226070192..226076477-chr1:226076711..226082534,9	K562	blood:
16	chr1:226054269..226057848-chr1:226069122..226072255,3	K562	blood:
17	chr1:226069701..226070650-chr5:442377..443321,2	Hela-S3	cervix:
18	chr1:225963541..225967644-chr1:226069236..226073918,5	MCF-7	breast:
19	chr1:226066440..226072029-chr1:226106315..226113044,10	MCF-7	breast:
20	chr1:226067470..226074101-chr1:226108823..226116408,13	MCF-7	breast:

Variant related genes	Relation type
TMEM63A	TF binding region
TMEM63A	CpG island
ENSG00000180104	Chromatin interaction
ENSG00000243709	Chromatin interaction
ENSG00000137767	Chromatin interaction
ENSG00000221990	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000213032	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000242861	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000143751	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10047091	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10158952	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12061043	0.95[EUR][1000 genomes]
rs12071072	0.95[EUR][1000 genomes]
rs12071104	0.95[EUR][1000 genomes]
rs12074209	0.95[EUR][1000 genomes]
rs12074247	0.95[EUR][1000 genomes]
rs12075664	0.95[EUR][1000 genomes]
rs2236143	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271544	1.00[EUR][1000 genomes]
rs2292556	0.95[EUR][1000 genomes]
rs2292559	0.95[EUR][1000 genomes]
rs2292561	0.95[EUR][1000 genomes]
rs2292568	0.92[EUR][1000 genomes]
rs28384446	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28384447	0.90[EUR][1000 genomes]
rs28384448	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738050	0.95[EUR][1000 genomes]
rs3738051	0.95[EUR][1000 genomes]
rs3753663	0.95[EUR][1000 genomes]
rs3753666	0.97[EUR][1000 genomes]
rs3753668	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753670	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766935	0.95[EUR][1000 genomes]
rs3766936	0.95[EUR][1000 genomes]
rs3766937	0.95[EUR][1000 genomes]
rs3766940	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3766941	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806257	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806258	0.95[EUR][1000 genomes]
rs41310561	0.95[EUR][1000 genomes]
rs4149227	0.92[EUR][1000 genomes]
rs4149228	0.95[EUR][1000 genomes]
rs4149230	0.95[EUR][1000 genomes]
rs45467394	0.90[EUR][1000 genomes]
rs56231004	0.95[EUR][1000 genomes]
rs56325807	0.95[EUR][1000 genomes]
rs57095220	0.95[EUR][1000 genomes]
rs57932384	0.95[EUR][1000 genomes]
rs59728172	0.95[EUR][1000 genomes]
rs60847271	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60943392	0.95[EUR][1000 genomes]
rs61033712	0.95[EUR][1000 genomes]
rs61227102	0.95[EUR][1000 genomes]
rs61295362	0.95[EUR][1000 genomes]
rs6664740	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74150536	0.95[EUR][1000 genomes]
rs7514448	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7516538	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv3354874	chr1:226069354-226072202	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 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	chr1:226067200-226071000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:226068600-226070600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
3	chr1:226068600-226071200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:226068600-226072000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:226068800-226071000	Active TSS	Lung	lung
6	chr1:226068800-226071200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:226068800-226071200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:226068800-226071200	Active TSS	Aorta	Aorta
9	chr1:226069000-226071000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr1:226069000-226071000	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr1:226069000-226071000	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr1:226069000-226071000	Active TSS	Small Intestine	intestine
13	chr1:226069000-226071200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:226069000-226071200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:226069000-226071200	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr1:226069000-226071200	Active TSS	Fetal Kidney	kidney
17	chr1:226069000-226071200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:226069000-226071200	Active TSS	Pancreas	Pancrea
19	chr1:226069000-226071400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr1:226069200-226070800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:226069200-226070800	Active TSS	Primary T cells from cord blood	blood
22	chr1:226069200-226071000	Active TSS	Stomach Mucosa	stomach
23	chr1:226069200-226071000	Bivalent/Poised TSS	HepG2	liver
24	chr1:226069200-226071000	Active TSS	HSMMtube	muscle
25	chr1:226069200-226071200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr1:226069200-226071200	Active TSS	Ovary	ovary
27	chr1:226069200-226071200	Active TSS	NHDF-Ad	bronchial
28	chr1:226069400-226070600	Active TSS	Primary T cells fromperipheralblood	blood
29	chr1:226069400-226070600	Active TSS	Colonic Mucosa	Colon
30	chr1:226069400-226070600	Active TSS	Thymus	Thymus
31	chr1:226069400-226070800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:226069400-226070800	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr1:226069400-226070800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr1:226069400-226070800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:226069400-226070800	Active TSS	Primary B cells from peripheral blood	blood
36	chr1:226069400-226070800	Active TSS	Brain Hippocampus Middle	brain
37	chr1:226069400-226070800	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr1:226069400-226070800	Active TSS	Spleen	Spleen
39	chr1:226069400-226070800	Active TSS	K562	blood
40	chr1:226069400-226070800	Active TSS	Osteobl	bone
41	chr1:226069400-226071000	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr1:226069400-226071000	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr1:226069400-226071000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:226069400-226071000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:226069400-226071000	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr1:226069400-226071000	Active TSS	Brain Angular Gyrus	brain
47	chr1:226069400-226071000	Active TSS	Brain Substantia Nigra	brain
48	chr1:226069400-226071000	Active TSS	Colon Smooth Muscle	Colon
49	chr1:226069400-226071000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:226069400-226071000	Active TSS	Fetal Intestine Large	intestine

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