Variant report

Variant	rs28365913
Chromosome Location	chr1:46016358-46016359
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	TCF12	chr1:46016097-46016722	GM12878	blood:	n/a	n/a
2	EGR1	chr1:46016189-46016742	MCF-7	breast:	n/a	chr1:46016480-46016494 chr1:46016482-46016496 chr1:46016484-46016493 chr1:46016484-46016494 chr1:46016484-46016494 chr1:46016483-46016490
3	RFX5	chr1:46016211-46016522	K562	blood:	n/a	n/a
4	NFIC	chr1:46015922-46016902	GM12878	blood:	n/a	n/a
5	CTCF	chr1:46016240-46016390	HRE	kidney:	n/a	n/a
6	MAZ	chr1:46016175-46017136	Hela-S3	cervix:	n/a	chr1:46016486-46016496 chr1:46016487-46016496 chr1:46016486-46016497 chr1:46016487-46016496 chr1:46016486-46016497 chr1:46016487-46016497 chr1:46016485-46016494 chr1:46016483-46016498 chr1:46016487-46016496 chr1:46016485-46016498
7	NFIC	chr1:46016089-46016887	ECC-1	luminal epithelium:	n/a	n/a
8	HCFC1	chr1:46016141-46016995	K562	blood:	n/a	n/a
9	ATF2	chr1:46016146-46016688	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:46016081-46017059	GM18951	blood:	n/a	n/a
11	POLR2A	chr1:46016055-46016913	HepG2	liver:	n/a	n/a
12	BRCA1	chr1:46016311-46016567	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:46016142-46016905	GM10847	blood:	n/a	n/a
14	TAF1	chr1:46016032-46016951	A549	lung:	n/a	n/a
15	POLR2A	chr1:46015987-46016986	GM12891	blood:	n/a	n/a
16	BHLHE40	chr1:46016204-46016876	HepG2	liver:	n/a	n/a
17	TAF1	chr1:46016216-46016849	H1-neurons	neurons:	n/a	n/a
18	SIN3AK20	chr1:46016103-46016963	SK-N-SH	brain:	n/a	n/a
19	BRCA1	chr1:46016192-46016745	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:46016064-46016927	H1-hESC	embryonic stem cell:	n/a	n/a
21	MBD4	chr1:46016045-46016844	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:46016129-46016882	A549	lung:	n/a	n/a
23	ARID3A	chr1:46016154-46016636	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:46016080-46016986	NB4	blood:	n/a	n/a
25	POLR2A	chr1:46016008-46017116	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr1:46015996-46016943	K562	blood:	n/a	n/a
27	E2F6	chr1:46016037-46016810	A549	lung:	n/a	chr1:46016465-46016475
28	ELF1	chr1:46016126-46016722	A549	lung:	n/a	n/a
29	SIN3AK20	chr1:46016212-46017127	PANC-1	pancreas:	n/a	n/a
30	CTCF	chr1:46016320-46016470	AG04450	lung:	n/a	n/a
31	POLR2A	chr1:46015874-46017118	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:46016076-46016886	HepG2	liver:	n/a	n/a
33	UBTF	chr1:46016271-46016779	K562	blood:	n/a	n/a
34	RFX5	chr1:46016173-46016875	Hela-S3	cervix:	n/a	n/a
35	USF1	chr1:46016168-46016889	A549	lung:	n/a	chr1:46016486-46016497
36	POLR2A	chr1:46016019-46017048	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:46016026-46016986	GM12892	blood:	n/a	n/a
38	MAX	chr1:46015945-46017017	A549	lung:	n/a	chr1:46016486-46016496 chr1:46016487-46016496 chr1:46016486-46016497 chr1:46016487-46016496 chr1:46016486-46016497 chr1:46016487-46016497 chr1:46016485-46016494 chr1:46016483-46016498 chr1:46016487-46016496 chr1:46016485-46016498
39	NR2F2	chr1:46015931-46017082	K562	blood:	n/a	n/a
40	YY1	chr1:46016227-46016686	H1-hESC	embryonic stem cell:	n/a	chr1:46016413-46016427 chr1:46016495-46016509
41	POLR2A	chr1:46016004-46016972	K562	blood:	n/a	n/a
42	REST	chr1:46016196-46016757	PANC-1	pancreas:	n/a	chr1:46016465-46016478
43	RCOR1	chr1:46016115-46017065	K562	blood:	n/a	n/a
44	SPI1	chr1:46016285-46016570	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:46016037-46017018	MCF-7	breast:	n/a	n/a
46	REST	chr1:46015904-46017227	H1-neurons	neurons:	n/a	chr1:46016465-46016478
47	POLR2A	chr1:46015911-46017012	U87	brain:	n/a	n/a
48	POLR2A	chr1:46016054-46016938	Hela-S3	cervix:	n/a	n/a
49	E2F4	chr1:46016224-46016888	MCF10A-Er-Src	breast:	n/a	chr1:46016465-46016475
50	MYC	chr1:46016231-46016753	GM12878	blood:	n/a	chr1:46016486-46016496 chr1:46016487-46016496 chr1:46016486-46016497 chr1:46016487-46016496 chr1:46016486-46016497 chr1:46016487-46016497 chr1:46016485-46016494 chr1:46016483-46016498 chr1:46016487-46016496 chr1:46016485-46016498

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:46016331-46016381	Hepatocyte	liver:	n/a
2	chr1:46016331-46016381	HRE	kidney:	n/a
3	chr1:46016331-46016381	GM12891	blood:	n/a
4	chr1:46016331-46016381	IMR90	lung:	fetal
5	chr1:46016349-46016399	NHDF-neo	bronchial:	n/a
6	chr1:46016349-46016399	HRCEpiC	kidney:	n/a
7	chr1:46016331-46016381	NB4	blood:	n/a
8	chr1:46016331-46016381	HepG2	liver:	n/a
9	chr1:46016331-46016381	GM12878	blood:	n/a
10	chr1:46016349-46016399	HCPEpiC	choroid plexus:	n/a
11	chr1:46016331-46016381	PFSK-1	brain:	n/a
12	chr1:46016349-46016399	ovcar-3	ovarian:	n/a
13	chr1:46016331-46016381	HCM	heart:	n/a
14	chr1:46016331-46016381	HRCEpiC	kidney:	n/a
15	chr1:46016331-46016381	NHBE	bronchial:	n/a
16	chr1:46016331-46016381	AG09319	gingival:	n/a
17	chr1:46016331-46016381	A549	lung:	n/a
18	chr1:46016349-46016399	HL-60	blood:	n/a
19	chr1:46016331-46016381	NHDF-neo	bronchial:	n/a
20	chr1:46016331-46016381	HCT-116	colon:	n/a
21	chr1:46016349-46016399	HCM	heart:	n/a
22	chr1:46016349-46016399	PANC-1	pancreas:	n/a
23	chr1:46016331-46016381	SKMC	muscle:	n/a
24	chr1:46016331-46016381	K562	blood:	n/a
25	chr1:46016331-46016381	HNPCEpiC	eye:	n/a
26	chr1:46016349-46016399	AG09309	skin:	n/a
27	chr1:46016349-46016399	AoSMC	blood vessel:	n/a
28	chr1:46016349-46016399	LNCaP	prostate:	n/a
29	chr1:46016331-46016381	Hela-S3	cervix:	n/a
30	chr1:46016349-46016399	AG04450	lung:	fetal
31	chr1:46016349-46016399	HCF	heart:	n/a
32	chr1:46016331-46016381	GM06990	blood:	n/a
33	chr1:46016349-46016399	NB4	blood:	n/a
34	chr1:46016349-46016399	CMK	blood:	n/a
35	chr1:46016349-46016399	GM19239	blood:	n/a
36	chr1:46016349-46016399	NT2-D1	testis:	n/a
37	chr1:46016331-46016381	U87	brain:	n/a
38	chr1:46016349-46016399	GM06990	blood:	n/a
39	chr1:46016349-46016399	U87	brain:	n/a
40	chr1:46016331-46016381	HCF	heart:	n/a
41	chr1:46016331-46016381	AG04449	skin:	fetal
42	chr1:46016331-46016381	SK-N-SH_RA	brain:	n/a
43	chr1:46016331-46016381	BE2_C	brain:	n/a
44	chr1:46016349-46016399	Hela-S3	cervix:	n/a
45	chr1:46016331-46016381	AoSMC	blood vessel:	n/a
46	chr1:46016331-46016381	MCF-7	breast:	n/a
47	chr1:46016349-46016399	HUVEC	blood vessel:	n/a
48	chr1:46016331-46016381	ECC-1	luminal epithelium:	n/a
49	chr1:46016349-46016399	Hepatocyte	liver:	n/a
50	chr1:46016349-46016399	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45476252..45479466-chr1:46015891..46017851,3	K562	blood:
2	chr1:46014904..46019071-chr1:46034504..46037164,4	K562	blood:
3	chr1:46012797..46020877-chr1:46047985..46055272,23	K562	blood:
4	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
5	chr1:45195042..45198446-chr1:46014587..46018125,4	K562	blood:
6	chr1:46014878..46016600-chr1:46048610..46051417,2	MCF-7	breast:
7	chr1:46015193..46018509-chr1:46048657..46051369,3	MCF-7	breast:
8	chr1:46015946..46016839-chr17:79479392..79480059,2	Hela-S3	cervix:
9	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
10	chr1:46016057..46016984-chr11:8704263..8704927,2	HCT-116	colon:
11	chr1:45974939..45977846-chr1:46015282..46017928,2	MCF-7	breast:
12	chr1:45184676..45187669-chr1:46014660..46016558,3	K562	blood:
13	chr1:45985342..45989391-chr1:46011113..46019467,18	MCF-7	breast:
14	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
15	chr1:46012228..46018632-chr1:46046407..46053601,17	K562	blood:
16	chr1:45986942..45987554-chr1:46016193..46016898,2	MCF-7	breast:
17	chr1:45271619..45273419-chr1:46014827..46017277,2	K562	blood:
18	chr1:46016158..46018280-chr1:46030299..46033160,3	K562	blood:
19	chr1:46014904..46020261-chr1:46034308..46041374,10	K562	blood:
20	chr1:45196137..45198081-chr1:46014587..46016947,2	K562	blood:
21	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:

Variant related genes	Relation type
AKR1A1	TF binding region
AKR1A1	CpG island
ENSG00000126107	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000184009	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2275084	1.00[EUR][1000 genomes]
rs2297652	1.00[EUR][1000 genomes]
rs28365868	1.00[EUR][1000 genomes]
rs3748645	1.00[EUR][1000 genomes]
rs3811433	1.00[EUR][1000 genomes]
rs3811434	1.00[EUR][1000 genomes]
rs41269109	1.00[EUR][1000 genomes]
rs41269111	1.00[EUR][1000 genomes]
rs41269115	1.00[EUR][1000 genomes]
rs41272133	1.00[EUR][1000 genomes]
rs41312018	1.00[EUR][1000 genomes]
rs56215132	1.00[EUR][1000 genomes]
rs56220330	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46015600-46017400	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:46015800-46016800	Active TSS	Brain Hippocampus Middle	brain
3	chr1:46015800-46016800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:46015800-46017000	Active TSS	Fetal Brain Female	brain
5	chr1:46015800-46017400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:46015800-46017400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:46016000-46016400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
8	chr1:46016000-46016400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:46016000-46016400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:46016000-46016400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:46016000-46016400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:46016000-46016400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:46016000-46016400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr1:46016000-46016400	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr1:46016000-46016400	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr1:46016000-46016400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr1:46016000-46016400	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr1:46016000-46016400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr1:46016000-46016400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr1:46016000-46016400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:46016000-46016400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr1:46016000-46016400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr1:46016000-46016400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr1:46016000-46016400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:46016000-46016400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:46016000-46016400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr1:46016000-46016400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr1:46016000-46016400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:46016000-46016400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:46016000-46016400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:46016000-46016400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr1:46016000-46016400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr1:46016000-46016400	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr1:46016000-46016400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr1:46016000-46016400	Flanking Active TSS	Fetal Intestine Large	intestine
36	chr1:46016000-46016400	Flanking Active TSS	Fetal Lung	lung
37	chr1:46016000-46016400	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr1:46016000-46016400	Flanking Active TSS	Placenta	Placenta
39	chr1:46016000-46016400	Flanking Active TSS	Fetal Thymus	thymus
40	chr1:46016000-46016400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr1:46016000-46016400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr1:46016000-46016400	Flanking Active TSS	Stomach Mucosa	stomach
43	chr1:46016000-46016400	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr1:46016000-46016400	Flanking Active TSS	Dnd41	blood
45	chr1:46016000-46016400	Flanking Active TSS	GM12878-XiMat	blood
46	chr1:46016000-46016400	Flanking Active TSS	Hela-S3	cervix
47	chr1:46016000-46016400	Flanking Active TSS	HepG2	liver
48	chr1:46016000-46016400	Flanking Active TSS	HMEC	breast
49	chr1:46016000-46016400	Flanking Active TSS	HUVEC	blood vessel
50	chr1:46016000-46016400	Flanking Active TSS	K562	blood

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