Variant report

Variant	rs28607905
Chromosome Location	chr1:46016501-46016502
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	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
6	NFIC	chr1:46016089-46016887	ECC-1	luminal epithelium:	n/a	n/a
7	HCFC1	chr1:46016141-46016995	K562	blood:	n/a	n/a
8	ATF2	chr1:46016146-46016688	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:46016081-46017059	GM18951	blood:	n/a	n/a
10	POLR2A	chr1:46016055-46016913	HepG2	liver:	n/a	n/a
11	BRCA1	chr1:46016311-46016567	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:46016142-46016905	GM10847	blood:	n/a	n/a
13	TAF1	chr1:46016032-46016951	A549	lung:	n/a	n/a
14	CTCF	chr1:46016500-46016650	AG09309	skin:	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	POLR2A	chr1:46015874-46017118	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:46016076-46016886	HepG2	liver:	n/a	n/a
32	UBTF	chr1:46016271-46016779	K562	blood:	n/a	n/a
33	RFX5	chr1:46016173-46016875	Hela-S3	cervix:	n/a	n/a
34	USF1	chr1:46016168-46016889	A549	lung:	n/a	chr1:46016486-46016497
35	POLR2A	chr1:46016019-46017048	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:46016026-46016986	GM12892	blood:	n/a	n/a
37	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
38	NR2F2	chr1:46015931-46017082	K562	blood:	n/a	n/a
39	YY1	chr1:46016227-46016686	H1-hESC	embryonic stem cell:	n/a	chr1:46016413-46016427 chr1:46016495-46016509
40	POLR2A	chr1:46016004-46016972	K562	blood:	n/a	n/a
41	REST	chr1:46016196-46016757	PANC-1	pancreas:	n/a	chr1:46016465-46016478
42	RCOR1	chr1:46016115-46017065	K562	blood:	n/a	n/a
43	SPI1	chr1:46016285-46016570	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:46016037-46017018	MCF-7	breast:	n/a	n/a
45	REST	chr1:46015904-46017227	H1-neurons	neurons:	n/a	chr1:46016465-46016478
46	POLR2A	chr1:46015911-46017012	U87	brain:	n/a	n/a
47	POLR2A	chr1:46016054-46016938	Hela-S3	cervix:	n/a	n/a
48	E2F4	chr1:46016224-46016888	MCF10A-Er-Src	breast:	n/a	chr1:46016465-46016475
49	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
50	NFATC1	chr1:46015920-46016733	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:46016473-46016523	NB4	blood:	n/a
2	chr1:46016485-46016535	NHDF-neo	bronchial:	n/a
3	chr1:46016485-46016535	SKMC	muscle:	n/a
4	chr1:46016485-46016535	ProgFib	skin:	n/a
5	chr1:46016485-46016535	GM06990	blood:	n/a
6	chr1:46016485-46016535	HNPCEpiC	eye:	n/a
7	chr1:46016473-46016523	HAEpiC	amniotic membrane:	n/a
8	chr1:46016473-46016523	HCM	heart:	n/a
9	chr1:46016473-46016523	Caco-2	colon:	n/a
10	chr1:46016473-46016523	SK-N-SH	brain:	n/a
11	chr1:46016485-46016535	HRPEpiC	eye:	n/a
12	chr1:46016485-46016535	LNCaP	prostate:	n/a
13	chr1:46016473-46016523	HMEC	breast:	n/a
14	chr1:46016473-46016523	PrEC	prostate:	n/a
15	chr1:46016473-46016523	U87	brain:	n/a
16	chr1:46016473-46016523	Jurkat	blood:	n/a
17	chr1:46016485-46016535	HCPEpiC	choroid plexus:	n/a
18	chr1:46016473-46016523	NH-A	brain:	n/a
19	chr1:46016485-46016535	AG04449	skin:	fetal
20	chr1:46016485-46016535	HMEC	breast:	n/a
21	chr1:46016485-46016535	GM12891	blood:	n/a
22	chr1:46016485-46016535	Caco-2	colon:	n/a
23	chr1:46016473-46016523	AG10803	skin:	n/a
24	chr1:46016485-46016535	NB4	blood:	n/a
25	chr1:46016485-46016535	HCM	heart:	n/a
26	chr1:46016485-46016535	HIPEpiC	eye:	n/a
27	chr1:46016473-46016523	HUVEC	blood vessel:	n/a
28	chr1:46016485-46016535	A549	lung:	n/a
29	chr1:46016485-46016535	RPTEC	kidney:	n/a
30	chr1:46016485-46016535	GM12878	blood:	n/a
31	chr1:46016473-46016523	LNCaP	prostate:	n/a
32	chr1:46016485-46016535	AG04450	lung:	fetal
33	chr1:46016473-46016523	AoSMC	blood vessel:	n/a
34	chr1:46016485-46016535	HEK293	kidney:	embryo
35	chr1:46016485-46016535	BE2_C	brain:	n/a
36	chr1:46016485-46016535	PANC-1	pancreas:	n/a
37	chr1:46016473-46016523	K562	blood:	n/a
38	chr1:46016473-46016523	HRE	kidney:	n/a
39	chr1:46016485-46016535	HAEpiC	amniotic membrane:	n/a
40	chr1:46016473-46016523	Hela-S3	cervix:	n/a
41	chr1:46016473-46016523	GM12891	blood:	n/a
42	chr1:46016485-46016535	SK-N-SH_RA	brain:	n/a
43	chr1:46016473-46016523	AG04449	skin:	fetal
44	chr1:46016485-46016535	GM19239	blood:	n/a
45	chr1:46016485-46016535	AG09319	gingival:	n/a
46	chr1:46016473-46016523	HRPEpiC	eye:	n/a
47	chr1:46016473-46016523	HPAEpiC	pulmonary alveolar:	n/a
48	chr1:46016473-46016523	HCF	heart:	n/a
49	chr1:46016473-46016523	SK-N-MC	brain:	n/a
50	chr1:46016485-46016535	HCT-116	colon:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45476252..45479466-chr1:46015891..46017851,3	K562	blood:
2	chr1:45986852..45988008-chr1:46016453..46017072,3	NB4	blood:
3	chr1:46014904..46019071-chr1:46034504..46037164,4	K562	blood:
4	chr1:46012797..46020877-chr1:46047985..46055272,23	K562	blood:
5	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
6	chr1:45195042..45198446-chr1:46014587..46018125,4	K562	blood:
7	chr1:46014878..46016600-chr1:46048610..46051417,2	MCF-7	breast:
8	chr1:46015193..46018509-chr1:46048657..46051369,3	MCF-7	breast:
9	chr1:46015946..46016839-chr17:79479392..79480059,2	Hela-S3	cervix:
10	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
11	chr1:46016057..46016984-chr11:8704263..8704927,2	HCT-116	colon:
12	chr1:45993856..45997631-chr1:46016442..46019336,3	K562	blood:
13	chr1:45974939..45977846-chr1:46015282..46017928,2	MCF-7	breast:
14	chr1:46016478..46017039-chr11:62608980..62609620,2	NB4	blood:
15	chr1:45184676..45187669-chr1:46014660..46016558,3	K562	blood:
16	chr1:45985342..45989391-chr1:46011113..46019467,18	MCF-7	breast:
17	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
18	chr1:46012228..46018632-chr1:46046407..46053601,17	K562	blood:
19	chr1:45986942..45987554-chr1:46016193..46016898,2	MCF-7	breast:
20	chr1:45271619..45273419-chr1:46014827..46017277,2	K562	blood:
21	chr1:46016158..46018280-chr1:46030299..46033160,3	K562	blood:
22	chr1:46014904..46020261-chr1:46034308..46041374,10	K562	blood:
23	chr1:45196137..45198081-chr1:46014587..46016947,2	K562	blood:
24	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:

Variant related genes	Relation type
AKR1A1	TF binding region
AKR1A1	CpG island
ENSG00000126107	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000234379	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000184009	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11211127	1.00[AMR][1000 genomes]
rs11211144	1.00[AMR][1000 genomes]
rs11211148	1.00[AMR][1000 genomes]
rs11211153	1.00[AMR][1000 genomes]
rs11211154	1.00[AMR][1000 genomes]
rs11211155	1.00[AMR][1000 genomes]
rs11211156	1.00[AMR][1000 genomes]
rs11211167	1.00[AMR][1000 genomes]
rs12057167	1.00[AMR][1000 genomes]
rs12060056	1.00[AMR][1000 genomes]
rs12061890	1.00[AMR][1000 genomes]
rs12062361	1.00[AMR][1000 genomes]
rs12063380	1.00[AMR][1000 genomes]
rs12064908	1.00[AMR][1000 genomes]
rs12067882	1.00[AMR][1000 genomes]
rs12070146	1.00[AMR][1000 genomes]
rs12070177	1.00[AMR][1000 genomes]
rs12073045	1.00[AMR][1000 genomes]
rs12073047	1.00[AMR][1000 genomes]
rs12073132	1.00[AMR][1000 genomes]
rs12077112	1.00[AMR][1000 genomes]
rs12080482	1.00[AMR][1000 genomes]
rs12081121	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12085372	1.00[AMR][1000 genomes]
rs12086880	1.00[AMR][1000 genomes]
rs12088810	1.00[AMR][1000 genomes]
rs12091335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091360	1.00[AMR][1000 genomes]
rs12093444	1.00[AMR][1000 genomes]
rs12094011	1.00[AMR][1000 genomes]
rs12097914	1.00[AMR][1000 genomes]
rs16832540	1.00[AMR][1000 genomes]
rs16832550	1.00[AMR][1000 genomes]
rs16832553	1.00[AMR][1000 genomes]
rs16832557	1.00[AMR][1000 genomes]
rs1691225	1.00[AMR][1000 genomes]
rs1691226	1.00[AMR][1000 genomes]
rs1691227	1.00[AMR][1000 genomes]
rs1762087	1.00[AMR][1000 genomes]
rs2782489	1.00[AMR][1000 genomes]
rs28532613	1.00[AMR][1000 genomes]
rs28548585	1.00[AMR][1000 genomes]
rs28576912	1.00[AMR][1000 genomes]
rs35067820	1.00[AMR][1000 genomes]
rs35808563	1.00[AMR][1000 genomes]
rs486346	1.00[AMR][1000 genomes]
rs505175	1.00[AMR][1000 genomes]
rs506094	1.00[AMR][1000 genomes]
rs525706	1.00[AMR][1000 genomes]
rs622296	1.00[AMR][1000 genomes]
rs635446	1.00[AMR][1000 genomes]
rs665014	1.00[AMR][1000 genomes]
rs668289	1.00[AMR][1000 genomes]
rs669417	1.00[AMR][1000 genomes]
rs680267	1.00[AMR][1000 genomes]
rs7550744	1.00[AMR][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:127 , 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	chr1:46016000-46016600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr1:46016000-46016600	Flanking Active TSS	Fetal Muscle Trunk	muscle
9	chr1:46016000-46017000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:46016000-46017000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:46016000-46017000	Active TSS	Brain Anterior Caudate	brain
12	chr1:46016000-46017000	Active TSS	Colon Smooth Muscle	Colon
13	chr1:46016000-46017000	Active TSS	Fetal Brain Male	brain
14	chr1:46016000-46017000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:46016000-46017200	Active TSS	Brain Cingulate Gyrus	brain
16	chr1:46016000-46017200	Active TSS	Brain Germinal Matrix	brain
17	chr1:46016000-46017200	Active TSS	Duodenum Mucosa	Duodenum
18	chr1:46016000-46017200	Active TSS	Placenta Amnion	Placenta Amnion
19	chr1:46016000-46017200	Active TSS	Rectal Smooth Muscle	rectum
20	chr1:46016000-46017400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:46016000-46017400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:46016000-46017400	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:46016000-46017400	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr1:46016000-46017400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:46016000-46017400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:46016000-46017400	Active TSS	Aorta	Aorta
27	chr1:46016000-46017400	Active TSS	Colonic Mucosa	Colon
28	chr1:46016000-46017400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr1:46016000-46017400	Active TSS	Ovary	ovary
30	chr1:46016000-46017400	Active TSS	Psoas Muscle	Psoas
31	chr1:46016000-46017400	Active TSS	NH-A	brain
32	chr1:46016000-46017400	Active TSS	NHDF-Ad	bronchial
33	chr1:46016000-46017600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr1:46016000-46017600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr1:46016000-46017600	Active TSS	Brain Angular Gyrus	brain
36	chr1:46016000-46017600	Active TSS	Brain Substantia Nigra	brain
37	chr1:46016000-46017600	Active TSS	Esophagus	oesophagus
38	chr1:46016000-46017600	Active TSS	Fetal Kidney	kidney
39	chr1:46016000-46017600	Active TSS	Left Ventricle	heart
40	chr1:46016000-46017600	Active TSS	Right Atrium	heart
41	chr1:46016000-46017600	Active TSS	Right Ventricle	heart
42	chr1:46016000-46017600	Active TSS	A549	lung
43	chr1:46016000-46017600	Active TSS	HSMM	muscle
44	chr1:46016000-46017600	Active TSS	HSMMtube	muscle
45	chr1:46016000-46017800	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr1:46016000-46017800	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr1:46016000-46017800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr1:46016000-46018000	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr1:46016000-46018000	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:46016000-46018000	Active TSS	Pancreas	Pancrea

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