Variant report

Variant	rs1884998
Chromosome Location	chr1:160070804-160070805
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	RFX5	chr1:160070790-160071175	Hela-S3	cervix:	n/a	n/a
2	RAD21	chr1:160070768-160071178	GM12878	blood:	n/a	chr1:160070944-160070963 chr1:160070945-160070959
3	MXI1	chr1:160070795-160071235	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr1:160070714-160071412	ECC-1	luminal epithelium:	n/a	chr1:160070944-160070963 chr1:160070945-160070959
5	YY1	chr1:160070795-160071347	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:160070799-160071084	GM10266	blood:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
7	CTCF	chr1:160070792-160071103	ECC-1	luminal epithelium:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
8	RAD21	chr1:160070703-160071307	IMR90	lung:	n/a	chr1:160070944-160070963 chr1:160070945-160070959
9	MAX	chr1:160070763-160071296	H1-hESC	embryonic stem cell:	n/a	chr1:160071055-160071065
10	CTCF	chr1:160070795-160071093	GM10248	blood:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
11	RAD21	chr1:160070742-160071127	SK-N-SH_RA	brain:	n/a	chr1:160070944-160070963 chr1:160070945-160070959
12	CTCF	chr1:160070713-160071270	K562	blood:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
13	CTCF	chr1:160070756-160071121	GM19239	blood:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
14	CTCF	chr1:160070775-160071118	HepG2	liver:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
15	MAX	chr1:160070583-160071339	HCT-116	colon:	n/a	chr1:160071055-160071065
16	CTCF	chr1:160070789-160071046	A549	lung:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
17	MYC	chr1:160070775-160071334	K562	blood:	n/a	chr1:160071055-160071065
18	EP300	chr1:160070693-160071151	HepG2	liver:	n/a	n/a
19	IRF4	chr1:160070703-160071232	GM12878	blood:	n/a	n/a
20	RFX5	chr1:160070720-160071119	HepG2	liver:	n/a	n/a
21	SMC3	chr1:160070515-160072207	SK-N-SH	brain:	n/a	chr1:160070945-160070959
22	RUNX3	chr1:160070702-160071206	GM12878	blood:	n/a	n/a
23	CTCF	chr1:160070721-160071136	SK-N-SH_RA	brain:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
24	RAD21	chr1:160070787-160071050	K562	blood:	n/a	chr1:160070944-160070963 chr1:160070945-160070959
25	MXI1	chr1:160070645-160071692	SK-N-SH	brain:	n/a	chr1:160071406-160071415
26	RAD21	chr1:160070757-160071185	HepG2	liver:	n/a	chr1:160070944-160070963 chr1:160070945-160070959
27	FOXA1	chr1:160070703-160071208	HepG2	liver:	n/a	n/a
28	RAD21	chr1:160070531-160071293	H1-hESC	embryonic stem cell:	n/a	chr1:160070944-160070963 chr1:160070945-160070959
29	MAX	chr1:160070780-160071354	MCF-7	breast:	n/a	chr1:160071055-160071065
30	YY1	chr1:160070799-160071118	GM12892	blood:	n/a	n/a
31	GTF2F1	chr1:160070785-160071080	H1-hESC	embryonic stem cell:	n/a	n/a
32	YY1	chr1:160070759-160071197	H1-hESC	embryonic stem cell:	n/a	n/a
33	SMC3	chr1:160070683-160071222	K562	blood:	n/a	chr1:160070945-160070959
34	CTCF	chr1:160070647-160071262	MCF-7	breast:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
35	GATA3	chr1:160070796-160071198	T-47D	breast:	n/a	chr1:160070856-160070866
36	YY1	chr1:160070735-160071210	GM12878	blood:	n/a	n/a
37	TEAD4	chr1:160070753-160071265	K562	blood:	n/a	n/a
38	CTCF	chr1:160070800-160070950	GM12870	blood:	n/a	n/a
39	CTCF	chr1:160070749-160071162	T-47D	breast:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
40	CTCF	chr1:160070779-160071140	GM12891	blood:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
41	CTCF	chr1:160070740-160070890	GM12872	blood:	n/a	n/a
42	RAD21	chr1:160070774-160071162	K562	blood:	n/a	chr1:160070944-160070963 chr1:160070945-160070959
43	POLR2A	chr1:160070772-160071050	HUVEC	blood vessel:	n/a	n/a
44	ZBTB7A	chr1:160070791-160071122	K562	blood:	n/a	n/a
45	MAX	chr1:160070744-160071298	H1-hESC	embryonic stem cell:	n/a	chr1:160071055-160071065
46	STAT5A	chr1:160070715-160071188	K562	blood:	n/a	n/a
47	CREB1	chr1:160070659-160071341	H1-hESC	embryonic stem cell:	n/a	n/a
48	SIN3AK20	chr1:160070790-160071162	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr1:160070705-160071186	HepG2	liver:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959
50	CTCF	chr1:160070355-160071363	HCT-116	colon:	n/a	chr1:160070943-160070961 chr1:160070945-160070966 chr1:160070944-160070960 chr1:160070946-160070959

No.	Distal block	Cell Line	Cell type
1	chr1:160070516..160071069-chr1:160221447..160222373,2	K562	blood:
2	chr1:160070551..160071445-chr1:160260910..160261809,5	MCF-7	breast:
3	chr1:160068705..160070888-chr1:160253691..160256574,2	MCF-7	breast:
4	chr1:160068906..160070835-chr1:160071784..160074235,2	K562	blood:
5	chr1:160070092..160072124-chr1:160188156..160190319,2	MCF-7	breast:
6	chr1:160068235..160071185-chr1:160084103..160086176,2	K562	blood:
7	chr1:160070519..160071380-chr1:160162531..160163309,3	MCF-7	breast:
8	chr1:160070546..160071742-chr1:160189080..160190292,10	MCF-7	breast:
9	chr1:160069512..160071291-chr1:160347356..160349425,2	K562	blood:
10	chr1:160070408..160071354-chr1:160345975..160346934,8	K562	blood:
11	chr1:160070477..160071561-chr1:160188657..160190008,7	MCF-7	breast:
12	chr1:160070559..160071355-chr1:160131889..160132803,3	K562	blood:
13	chr1:160070686..160071362-chr1:160385867..160386408,2	MCF-7	breast:
14	chr1:160069814..160072169-chr1:160152055..160154283,2	K562	blood:
15	chr1:160070040..160071802-chr1:160346010..160346771,4	MCF-7	breast:
16	chr1:160070501..160071427-chr1:160189109..160189635,3	K562	blood:
17	chr1:160068738..160071829-chr1:160174520..160176851,4	MCF-7	breast:
18	chr1:160070492..160071341-chr2:153031455..153032447,2	MCF-7	breast:
19	chr1:160054860..160056008-chr1:160070687..160071423,4	MCF-7	breast:
20	chr1:160070533..160071666-chr1:160261031..160261788,4	MCF-7	breast:
21	chr1:160069126..160071871-chr1:160230770..160232513,2	MCF-7	breast:

Variant related genes	Relation type
IGSF8	TF binding region
ENSG00000228606	Chromatin interaction
ENSG00000162735	Chromatin interaction
ENSG00000258465	Chromatin interaction
ENSG00000265381	Chromatin interaction
ENSG00000018625	Chromatin interaction
ENSG00000162734	Chromatin interaction
ENSG00000115145	Chromatin interaction
ENSG00000132716	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11265317	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1131891	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1186675	0.83[EUR][1000 genomes]
rs12401984	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12402134	0.84[EUR][1000 genomes]
rs12402888	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12408584	0.83[EUR][1000 genomes]
rs12727520	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1321653	0.88[AFR][1000 genomes]
rs3747619	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41265757	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55753565	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56187338	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211999	0.83[EUR][1000 genomes]
rs59366803	0.86[AFR][1000 genomes]
rs61822013	0.83[EUR][1000 genomes]
rs61822015	0.83[EUR][1000 genomes]
rs970365	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv520189	chr1:160011512-160095625	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1806746	chr1:160029416-160105927	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824420	chr1:160029416-160105927	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1843994	chr1:160029416-160105927	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv534066	chr1:160029416-160105986	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv1794281	chr1:160029416-160111565	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv1820784	chr1:160029416-160159395	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv534165	chr1:160029416-160187302	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160068400-160071000	Weak transcription	Gastric	stomach
2	chr1:160068400-160071200	Weak transcription	Aorta	Aorta
3	chr1:160068400-160071200	Weak transcription	Lung	lung
4	chr1:160068400-160071200	Weak transcription	Spleen	Spleen
5	chr1:160069200-160071000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:160069200-160071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:160069200-160071000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:160069200-160071000	Weak transcription	Esophagus	oesophagus
9	chr1:160069200-160071000	Weak transcription	Ovary	ovary
10	chr1:160069200-160074800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:160069400-160071000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:160069400-160071000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:160069400-160071000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:160069400-160071000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:160069400-160071000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:160069400-160071000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:160069400-160071000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:160069400-160071000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:160069400-160071000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:160069400-160071000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:160069400-160071000	Weak transcription	Adipose Nuclei	Adipose
22	chr1:160069400-160071000	Weak transcription	Brain Germinal Matrix	brain
23	chr1:160069400-160071000	Weak transcription	Fetal Intestine Small	intestine
24	chr1:160069400-160071000	Weak transcription	Fetal Kidney	kidney
25	chr1:160069400-160071000	Weak transcription	Fetal Stomach	stomach
26	chr1:160069400-160071000	Weak transcription	Left Ventricle	heart
27	chr1:160069400-160071000	Weak transcription	Psoas Muscle	Psoas
28	chr1:160069400-160071000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:160069400-160071000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:160069400-160071000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:160069400-160071000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr1:160069400-160071000	Weak transcription	Hela-S3	cervix
33	chr1:160069400-160071000	Weak transcription	HMEC	breast
34	chr1:160069400-160071000	Weak transcription	HSMM	muscle
35	chr1:160069400-160071000	Weak transcription	HSMMtube	muscle
36	chr1:160069400-160071000	Weak transcription	NHDF-Ad	bronchial
37	chr1:160069400-160071000	Weak transcription	NHLF	lung
38	chr1:160069400-160071000	Weak transcription	Osteobl	bone
39	chr1:160069400-160071200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:160069400-160071200	Enhancers	Brain Hippocampus Middle	brain
41	chr1:160069400-160071200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:160069400-160071200	Weak transcription	Right Atrium	heart
43	chr1:160069400-160071200	Weak transcription	Right Ventricle	heart
44	chr1:160069400-160071400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:160069400-160071600	Enhancers	Primary B cells from cord blood	blood
46	chr1:160069400-160071600	Enhancers	Primary B cells from peripheral blood	blood
47	chr1:160069400-160071600	Enhancers	Liver	Liver
48	chr1:160069400-160071800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr1:160069400-160072000	Enhancers	Primary T cells fromperipheralblood	blood
50	chr1:160069400-160072400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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