Variant report

Variant	rs73039980
Chromosome Location	chr1:179923297-179923298
allele	C/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	CTCF	chr1:179923160-179923310	AG04449	skin:	n/a	n/a
2	EP300	chr1:179923122-179923996	K562	blood:	n/a	n/a
3	STAT5A	chr1:179923180-179924684	GM12878	blood:	n/a	chr1:179924661-179924672
4	CUX1	chr1:179922861-179923983	K562	blood:	n/a	n/a
5	MXI1	chr1:179923279-179924088	K562	blood:	n/a	n/a
6	TBP	chr1:179923037-179924156	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr1:179922826-179923321	K562	blood:	n/a	n/a
8	MAX	chr1:179923235-179923921	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr1:179923200-179923350	HAc	cerebellar:	n/a	n/a
10	POLR2A	chr1:179923102-179924192	HCT-116	colon:	n/a	n/a
11	RELA	chr1:179923013-179924196	GM12892	blood:	n/a	n/a
12	CTCF	chr1:179923180-179923330	HRPEpiC	eye:	n/a	n/a
13	GATA3	chr1:179923011-179924448	MCF-7	breast:	n/a	chr1:179923862-179923870
14	CREB1	chr1:179923046-179924226	K562	blood:	n/a	n/a
15	SIX5	chr1:179923194-179924126	A549	lung:	n/a	n/a
16	CTCF	chr1:179923180-179923330	BE2_C	brain:	n/a	n/a
17	HCFC1	chr1:179922958-179924616	K562	blood:	n/a	n/a
18	ATF2	chr1:179923025-179924021	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:179923107-179924679	K562	blood:	n/a	n/a
20	CHD2	chr1:179923126-179924342	H1-hESC	embryonic stem cell:	n/a	chr1:179923854-179923863 chr1:179923879-179923889
21	POLR2A	chr1:179922854-179924621	K562	blood:	n/a	n/a
22	NFIC	chr1:179923295-179924151	HepG2	liver:	n/a	n/a
23	ELK1	chr1:179922824-179924151	K562	blood:	n/a	n/a
24	CEBPB	chr1:179923113-179923489	HepG2	liver:	n/a	chr1:179923270-179923281
25	MYC	chr1:179922868-179925091	K562	blood:	n/a	chr1:179924517-179924527
26	CTCF	chr1:179923160-179923310	HVMF	connective:	n/a	n/a
27	JUND	chr1:179923005-179925026	K562	blood:	n/a	chr1:179923759-179923773 chr1:179924900-179924912
28	TBP	chr1:179922869-179924160	GM12878	blood:	n/a	n/a
29	BRCA1	chr1:179923157-179924686	Hela-S3	cervix:	n/a	chr1:179923854-179923863
30	CTCF	chr1:179923260-179923410	HFF-Myc	foreskin:	n/a	n/a
31	CTCF	chr1:179923200-179923350	NHDF-neo	bronchial:	n/a	n/a
32	POLR2A	chr1:179923164-179924572	GM12878	blood:	n/a	n/a
33	CTCF	chr1:179923180-179923330	GM12871	blood:	n/a	n/a
34	CEBPB	chr1:179923066-179924060	K562	blood:	n/a	chr1:179923270-179923281
35	TCF7L2	chr1:179922851-179924697	HCT-116	colon:	n/a	n/a
36	YY1	chr1:179923293-179924527	H1-hESC	embryonic stem cell:	n/a	chr1:179923734-179923751 chr1:179923728-179923750 chr1:179923790-179923812 chr1:179924372-179924386 chr1:179923801-179923809 chr1:179923795-179923814 chr1:179923739-179923748
37	MAX	chr1:179922925-179924320	A549	lung:	n/a	n/a
38	ARID3A	chr1:179922891-179924082	K562	blood:	n/a	chr1:179923849-179923864
39	CUX1	chr1:179922957-179924019	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:179922802-179924248	PFSK-1	brain:	n/a	n/a
41	CTCF	chr1:179923160-179923310	HPAF	blood vessel:	n/a	n/a
42	POLR2A	chr1:179923144-179924441	GM12892	blood:	n/a	n/a
43	POLR2A	chr1:179922923-179924795	GM12878	blood:	n/a	n/a
44	CTCF	chr1:179923180-179923330	HA-sp	spinal cord:	n/a	n/a
45	MYC	chr1:179922890-179924005	MCF10A-Er-Src	breast:	n/a	n/a
46	CREB1	chr1:179923259-179924264	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAZ	chr1:179922884-179924760	K562	blood:	n/a	chr1:179924517-179924527
48	MTA3	chr1:179922795-179923980	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:179923261-179924386	HEK293	kidney:	n/a	n/a
50	IRF1	chr1:179922968-179924148	K562	blood:	n/a	chr1:179923656-179923667

No.	Distal block	Cell Line	Cell type
1	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:
2	chr1:179922632..179924837-chr10:27530640..27532515,2	MCF-7	breast:
3	chr1:179922139..179925093-chr1:180123797..180126783,3	K562	blood:
4	chr1:179921069..179927710-chr1:179937007..179944258,10	K562	blood:
5	chr1:179849016..179853452-chr1:179922333..179928502,16	K562	blood:
6	chr1:179921867..179924634-chr1:180042656..180044466,2	MCF-7	breast:
7	chr1:179847679..179853408-chr1:179922379..179926886,15	MCF-7	breast:
8	chr1:179923170..179924133-chr2:73461202..73461919,2	NB4	blood:
9	chr1:179922809..179925375-chr1:180469288..180472844,3	MCF-7	breast:
10	chr1:179909218..179916721-chr1:179922197..179926382,9	K562	blood:
11	chr1:179909514..179912296-chr1:179922909..179924946,2	MCF-7	breast:
12	chr1:179842979..179846933-chr1:179922588..179926684,5	K562	blood:
13	chr1:179906513..179911873-chr1:179922155..179925771,5	K562	blood:
14	chr1:179848142..179854405-chr1:179919774..179927189,17	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TOR1AIP2-4	chr1:179922319-179923575	ENSG00000260360.1

Variant related genes	Relation type
CEP350	TF binding region
ENSG00000261831	Chromatin interaction
ENSG00000235145	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000107897	Chromatin interaction
ENSG00000262412	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000135624	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000135847	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000169905	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs3842887	0.81[AFR][1000 genomes]
rs57875912	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58605404	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59265893	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59508309	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60065834	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60495007	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60594364	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61554984	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032361	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032364	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032365	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032367	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032369	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032376	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032384	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032387	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032389	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032395	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032399	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034469	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034472	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034474	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034477	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034478	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034489	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034495	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036405	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036409	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036413	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036425	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036432	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036436	0.92[AFR][1000 genomes]
rs73036437	0.92[AFR][1000 genomes]
rs73036439	0.88[AFR][1000 genomes]
rs73036466	0.81[AFR][1000 genomes]
rs73039985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73039997	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73041713	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 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	chr1:179920800-179923600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr1:179922600-179923400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
3	chr1:179922600-179923400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr1:179922600-179923400	Flanking Active TSS	Dnd41	blood
5	chr1:179922600-179923600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr1:179922600-179923600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr1:179922600-179923600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr1:179922600-179923600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:179922600-179923600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:179922600-179923600	Flanking Active TSS	GM12878-XiMat	blood
11	chr1:179922600-179923800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr1:179922600-179925400	Active TSS	Colonic Mucosa	Colon
13	chr1:179922600-179926000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:179922800-179923400	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr1:179922800-179923400	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr1:179922800-179923400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr1:179922800-179923400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr1:179922800-179923400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr1:179922800-179923400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:179922800-179923400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:179922800-179923400	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr1:179922800-179923400	Flanking Active TSS	Fetal Brain Male	brain
23	chr1:179922800-179923400	Flanking Active TSS	Fetal Intestine Small	intestine
24	chr1:179922800-179923400	Flanking Active TSS	NH-A	brain
25	chr1:179922800-179923600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr1:179922800-179923600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:179922800-179923600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:179922800-179923600	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr1:179922800-179923600	Active TSS	Fetal Heart	heart
30	chr1:179922800-179923600	Flanking Active TSS	Fetal Thymus	thymus
31	chr1:179922800-179923600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr1:179922800-179923600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr1:179922800-179923600	Flanking Active TSS	HMEC	breast
34	chr1:179922800-179923600	Flanking Active TSS	HUVEC	blood vessel
35	chr1:179922800-179923600	Flanking Active TSS	K562	blood
36	chr1:179922800-179923600	Flanking Active TSS	NHEK	skin
37	chr1:179922800-179923600	Flanking Active TSS	Osteobl	bone
38	chr1:179922800-179923800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr1:179922800-179923800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:179922800-179923800	Active TSS	Right Atrium	heart
41	chr1:179922800-179923800	Flanking Active TSS	Hela-S3	cervix
42	chr1:179922800-179924800	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr1:179922800-179924800	Active TSS	Brain Cingulate Gyrus	brain
44	chr1:179922800-179924800	Active TSS	Brain Hippocampus Middle	brain
45	chr1:179922800-179924800	Active TSS	Fetal Brain Female	brain
46	chr1:179922800-179924800	Active TSS	Pancreas	Pancrea
47	chr1:179922800-179925000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr1:179922800-179925000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:179922800-179925000	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:179922800-179925200	Active TSS	H9 Cell Line	embryonic stem cell

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