Variant report

Variant	rs668289
Chromosome Location	chr1:46016153-46016154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:337)
CpG islands
(count:61)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:337 , 50 per page) page: 1 2 3 4 5 6 7

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	NFIC	chr1:46015922-46016902	GM12878	blood:	n/a	n/a
3	CTCF	chr1:46016100-46016250	RPTEC	kidney:	n/a	n/a
4	NFIC	chr1:46016089-46016887	ECC-1	luminal epithelium:	n/a	n/a
5	HCFC1	chr1:46016141-46016995	K562	blood:	n/a	n/a
6	CTCF	chr1:46016100-46016250	GM12868	blood:	n/a	n/a
7	ATF2	chr1:46016146-46016688	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:46016081-46017059	GM18951	blood:	n/a	n/a
9	POLR2A	chr1:46016055-46016913	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:46016142-46016905	GM10847	blood:	n/a	n/a
11	TAF1	chr1:46016032-46016951	A549	lung:	n/a	n/a
12	POLR2A	chr1:46015987-46016986	GM12891	blood:	n/a	n/a
13	SIN3AK20	chr1:46016103-46016963	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr1:46016100-46016250	GM12872	blood:	n/a	n/a
15	POLR2A	chr1:46016064-46016927	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:46016081-46016208	A549	lung:	n/a	n/a
17	MBD4	chr1:46016045-46016844	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:46016129-46016882	A549	lung:	n/a	n/a
19	POLR2A	chr1:46016080-46016986	NB4	blood:	n/a	n/a
20	POLR2A	chr1:46016008-46017116	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:46015996-46016943	K562	blood:	n/a	n/a
22	E2F6	chr1:46016037-46016810	A549	lung:	n/a	chr1:46016465-46016475
23	ELF1	chr1:46016126-46016722	A549	lung:	n/a	n/a
24	POLR2A	chr1:46015874-46017118	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:46016076-46016886	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:46016019-46017048	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:46016026-46016986	GM12892	blood:	n/a	n/a
28	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
29	NR2F2	chr1:46015931-46017082	K562	blood:	n/a	n/a
30	POLR2A	chr1:46016004-46016972	K562	blood:	n/a	n/a
31	RCOR1	chr1:46016115-46017065	K562	blood:	n/a	n/a
32	POLR2A	chr1:46016037-46017018	MCF-7	breast:	n/a	n/a
33	REST	chr1:46015904-46017227	H1-neurons	neurons:	n/a	chr1:46016465-46016478
34	POLR2A	chr1:46015911-46017012	U87	brain:	n/a	n/a
35	CTCF	chr1:46016140-46016290	AG10803	skin:	n/a	n/a
36	POLR2A	chr1:46016054-46016938	Hela-S3	cervix:	n/a	n/a
37	NFATC1	chr1:46015920-46016733	GM12878	blood:	n/a	n/a
38	MAX	chr1:46016018-46016998	ECC-1	luminal epithelium:	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	GTF2F1	chr1:46016117-46016806	H1-hESC	embryonic stem cell:	n/a	n/a
40	PML	chr1:46016115-46016778	MCF-7	breast:	n/a	n/a
41	POLR2A	chr1:46016048-46016982	HUVEC	blood vessel:	n/a	n/a
42	CTCF	chr1:46016133-46016840	K562	blood:	n/a	n/a
43	E2F6	chr1:46016047-46016861	H1-hESC	embryonic stem cell:	n/a	chr1:46016465-46016475
44	MAX	chr1:46016085-46017065	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
45	E2F6	chr1:46016046-46016654	K562	blood:	n/a	chr1:46016465-46016475
46	TEAD4	chr1:46015968-46017543	K562	blood:	n/a	n/a
47	TAF1	chr1:46016150-46016966	MCF-7	breast:	n/a	n/a
48	POLR2A	chr1:46016125-46017013	GM18526	blood:	n/a	n/a
49	PML	chr1:46016028-46016909	K562	blood:	n/a	n/a
50	POLR2A	chr1:46015981-46017052	HCT-116	colon:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:46016123-46016173	A549	lung:	n/a
2	chr1:46016123-46016173	AG09309	skin:	n/a
3	chr1:46016123-46016173	NH-A	brain:	n/a
4	chr1:46016123-46016173	SK-N-MC	brain:	n/a
5	chr1:46016123-46016173	GM12892	blood:	n/a
6	chr1:46016123-46016173	NHDF-neo	bronchial:	n/a
7	chr1:46016123-46016173	SK-N-SH_RA	brain:	n/a
8	chr1:46016123-46016173	NHBE	bronchial:	n/a
9	chr1:46016123-46016173	HCT-116	colon:	n/a
10	chr1:46016123-46016173	HMEC	breast:	n/a
11	chr1:46016123-46016173	HAEpiC	amniotic membrane:	n/a
12	chr1:46016123-46016173	SK-N-SH	brain:	n/a
13	chr1:46016123-46016173	LNCaP	prostate:	n/a
14	chr1:46016123-46016173	HNPCEpiC	eye:	n/a
15	chr1:46016123-46016173	AG04449	skin:	fetal
16	chr1:46016123-46016173	GM12878	blood:	n/a
17	chr1:46016123-46016173	Caco-2	colon:	n/a
18	chr1:46016123-46016173	MCF10A-Er-Src	breast:	n/a
19	chr1:46016123-46016173	MCF-7	breast:	n/a
20	chr1:46016123-46016173	SKMC	muscle:	n/a
21	chr1:46016123-46016173	GM12891	blood:	n/a
22	chr1:46016123-46016173	ECC-1	luminal epithelium:	n/a
23	chr1:46016123-46016173	T-47D	breast:	n/a
24	chr1:46016123-46016173	U87	brain:	n/a
25	chr1:46016123-46016173	HCM	heart:	n/a
26	chr1:46016123-46016173	HIPEpiC	eye:	n/a
27	chr1:46016123-46016173	HRPEpiC	eye:	n/a
28	chr1:46016123-46016173	CMK	blood:	n/a
29	chr1:46016123-46016173	HCF	heart:	n/a
30	chr1:46016123-46016173	Hela-S3	cervix:	n/a
31	chr1:46016123-46016173	BE2_C	brain:	n/a
32	chr1:46016123-46016173	GM06990	blood:	n/a
33	chr1:46016123-46016173	PFSK-1	brain:	n/a
34	chr1:46016123-46016173	NB4	blood:	n/a
35	chr1:46016123-46016173	GM19239	blood:	n/a
36	chr1:46016123-46016173	H1-hESC	embryonic stem cell:	embryo
37	chr1:46016123-46016173	ProgFib	skin:	n/a
38	chr1:46016123-46016173	BJ	skin:	n/a
39	chr1:46016123-46016173	HCPEpiC	choroid plexus:	n/a
40	chr1:46016123-46016173	PrEC	prostate:	n/a
41	chr1:46016123-46016173	HPAEpiC	pulmonary alveolar:	n/a
42	chr1:46016123-46016173	AG09319	gingival:	n/a
43	chr1:46016123-46016173	HL-60	blood:	n/a
44	chr1:46016123-46016173	HUVEC	blood vessel:	n/a
45	chr1:46016123-46016173	AG10803	skin:	n/a
46	chr1:46016123-46016173	ovcar-3	ovarian:	n/a
47	chr1:46016123-46016173	PANC-1	pancreas:	n/a
48	chr1:46016123-46016173	NT2-D1	testis:	n/a
49	chr1:46016123-46016173	Hepatocyte	liver:	n/a
50	chr1:46016123-46016173	HEK293	kidney:	embryo

(count:19 , 50 per page) page: 1

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	chr1:45271619..45273419-chr1:46014827..46017277,2	K562	blood:
17	chr1:46014904..46020261-chr1:46034308..46041374,10	K562	blood:
18	chr1:45196137..45198081-chr1:46014587..46016947,2	K562	blood:
19	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:

No data

Variant related genes	Relation type
AKR1A1	TF binding region
AKR1A1	CpG island
ENSG00000117450	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000184009	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000236624	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	0.88[MKK][hapmap];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	1.00[AMR][1000 genomes]
rs12082672	1.00[YRI][hapmap];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[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1691226	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1691227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1762087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2782489	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28532613	1.00[AMR][1000 genomes]
rs28548585	1.00[AMR][1000 genomes]
rs28576912	0.88[MKK][hapmap];1.00[AMR][1000 genomes]
rs28607905	1.00[AMR][1000 genomes]
rs35067820	1.00[AMR][1000 genomes]
rs35808563	1.00[AMR][1000 genomes]
rs486346	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs505175	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs506094	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs525706	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs622296	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs635446	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs665014	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs669417	1.00[ASW][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs680267	1.00[YRI][hapmap];1.00[AFR][1000 genomes];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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46010200-46016200	Weak transcription	Small Intestine	intestine
2	chr1:46011000-46016200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:46014000-46016200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:46014000-46016200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:46015600-46017400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr1:46015800-46016200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:46015800-46016800	Active TSS	Brain Hippocampus Middle	brain
8	chr1:46015800-46016800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:46015800-46017000	Active TSS	Fetal Brain Female	brain
10	chr1:46015800-46017400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:46015800-46017400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:46016000-46016200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:46016000-46016200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:46016000-46016200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:46016000-46016200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:46016000-46016200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:46016000-46016200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:46016000-46016200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:46016000-46016200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:46016000-46016200	Flanking Active TSS	Liver	Liver
21	chr1:46016000-46016200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr1:46016000-46016200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr1:46016000-46016200	Enhancers	Fetal Heart	heart
24	chr1:46016000-46016200	Flanking Active TSS	Fetal Intestine Small	intestine
25	chr1:46016000-46016200	Flanking Active TSS	Fetal Stomach	stomach
26	chr1:46016000-46016200	Enhancers	Lung	lung
27	chr1:46016000-46016200	Flanking Active TSS	Thymus	Thymus
28	chr1:46016000-46016400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
29	chr1:46016000-46016400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:46016000-46016400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr1:46016000-46016400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:46016000-46016400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:46016000-46016400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:46016000-46016400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr1:46016000-46016400	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr1:46016000-46016400	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr1:46016000-46016400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr1:46016000-46016400	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr1:46016000-46016400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr1:46016000-46016400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr1:46016000-46016400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:46016000-46016400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr1:46016000-46016400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr1:46016000-46016400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr1:46016000-46016400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:46016000-46016400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:46016000-46016400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr1:46016000-46016400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr1:46016000-46016400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:46016000-46016400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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