Variant report

Variant	rs833824
Chromosome Location	chr12:49350430-49350431
allele	C/T
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	STAT1	chr12:49350341-49350823	GM12878	blood:	n/a	chr12:49350687-49350699 chr12:49350681-49350693 chr12:49350607-49350619 chr12:49350626-49350638
2	MYC	chr12:49350399-49351491	NB4	blood:	n/a	chr12:49350980-49350989
3	REST	chr12:49350299-49350526	K562	blood:	n/a	n/a
4	ZBTB33	chr12:49350084-49351698	HCT-116	colon:	n/a	chr12:49351310-49351325 chr12:49351348-49351357 chr12:49350999-49351009 chr12:49351346-49351356 chr12:49351343-49351358 chr12:49351349-49351359
5	MAX	chr12:49350168-49350815	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZKSCAN1	chr12:49350353-49350627	Hela-S3	cervix:	n/a	n/a
7	FOSL2	chr12:49350309-49351465	A549	lung:	n/a	n/a
8	RFX5	chr12:49350217-49350449	GM12878	blood:	n/a	n/a
9	CREB1	chr12:49349976-49350632	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr12:49349758-49351771	ECC-1	luminal epithelium:	n/a	chr12:49350980-49350989
11	POLR2A	chr12:49350393-49350704	HUVEC	blood vessel:	n/a	n/a
12	RCOR1	chr12:49350019-49351660	K562	blood:	n/a	n/a
13	TAF1	chr12:49350155-49351699	ECC-1	luminal epithelium:	n/a	n/a
14	TAF1	chr12:49350154-49350692	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:49350125-49350742	HCT-116	colon:	n/a	n/a
16	POLR2A	chr12:49349896-49350887	H1-hESC	embryonic stem cell:	n/a	n/a
17	EGR1	chr12:49349983-49351063	MCF-7	breast:	n/a	chr12:49350874-49350887 chr12:49350389-49350402 chr12:49350752-49350765 chr12:49350389-49350402 chr12:49350388-49350402 chr12:49350390-49350399 chr12:49350386-49350400 chr12:49350626-49350641 chr12:49350881-49350894 chr12:49350390-49350400 chr12:49350751-49350766 chr12:49350911-49350924 chr12:49350389-49350402 chr12:49350384-49350406 chr12:49350911-49350924 chr12:49350752-49350765 chr12:49350389-49350402 chr12:49350911-49350924
18	ELF1	chr12:49349738-49351783	MCF-7	breast:	n/a	chr12:49350992-49351004
19	POLR2A	chr12:49350189-49351743	U87	brain:	n/a	n/a
20	TCF12	chr12:49350059-49351854	ECC-1	luminal epithelium:	n/a	chr12:49351515-49351523
21	SPI1	chr12:49350301-49350499	K562	blood:	n/a	n/a
22	POLR2A	chr12:49350303-49350725	HCT-116	colon:	n/a	n/a
23	MYC	chr12:49350316-49350750	MCF10A-Er-Src	breast:	n/a	n/a
24	RFX5	chr12:49349847-49350459	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr12:49350175-49351738	HUVEC	blood vessel:	n/a	n/a
26	MYC	chr12:49350289-49350975	H1-hESC	embryonic stem cell:	n/a	n/a
27	RCOR1	chr12:49349930-49350912	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr12:49350015-49350670	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:49350041-49351803	H1-neurons	neurons:	n/a	n/a
30	MAX	chr12:49350183-49350723	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr12:49350017-49350812	SK-N-SH	brain:	n/a	n/a
32	REST	chr12:49350227-49350762	K562	blood:	n/a	n/a
33	POLR2A	chr12:49350144-49351648	MCF-7	breast:	n/a	n/a
34	POLR2A	chr12:49349992-49351649	H1-hESC	embryonic stem cell:	n/a	n/a
35	TAF1	chr12:49349842-49350692	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr12:49350418-49351662	Raji	blood:	n/a	n/a
37	GABPA	chr12:49350027-49350734	MCF-7	breast:	n/a	n/a
38	MAZ	chr12:49350346-49350529	HepG2	liver:	n/a	n/a
39	BRCA1	chr12:49350176-49351896	Hela-S3	cervix:	n/a	chr12:49351348-49351357
40	ZBTB7A	chr12:49350197-49351845	ECC-1	luminal epithelium:	n/a	n/a
41	SIN3AK20	chr12:49350063-49350845	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr12:49350030-49350689	K562	blood:	n/a	n/a
43	MYC	chr12:49350160-49351466	K562	blood:	n/a	chr12:49350980-49350989
44	EGR1	chr12:49350022-49351754	ECC-1	luminal epithelium:	n/a	chr12:49350874-49350887 chr12:49350389-49350402 chr12:49350752-49350765 chr12:49350389-49350402 chr12:49350388-49350402 chr12:49350390-49350399 chr12:49350386-49350400 chr12:49350626-49350641 chr12:49350881-49350894 chr12:49350390-49350400 chr12:49350751-49350766 chr12:49350911-49350924 chr12:49350389-49350402 chr12:49350384-49350406 chr12:49350911-49350924 chr12:49350752-49350765 chr12:49350389-49350402 chr12:49350911-49350924
45	ELF1	chr12:49350103-49350476	HepG2	liver:	n/a	n/a
46	HCFC1	chr12:49350356-49350730	K562	blood:	n/a	n/a
47	POLR2A	chr12:49350038-49350839	PFSK-1	brain:	n/a	n/a
48	YY1	chr12:49349732-49350820	H1-hESC	embryonic stem cell:	n/a	chr12:49350284-49350306
49	POLR2A	chr12:49349890-49351661	ECC-1	luminal epithelium:	n/a	n/a
50	YY1	chr12:49349761-49350707	H1-hESC	embryonic stem cell:	n/a	chr12:49350284-49350306

No.	Distal block	Cell Line	Cell type
1	chr12:49210476..49213723-chr12:49348025..49351364,4	MCF-7	breast:
2	chr12:49349835..49352133-chr12:49390670..49393580,2	K562	blood:
3	chr12:49326822..49334011-chr12:49345841..49353556,12	MCF-7	breast:
4	chr12:49319039..49321186-chr12:49348048..49350961,2	MCF-7	breast:
5	chr12:49349202..49351999-chr12:49410599..49414055,4	MCF-7	breast:
6	chr12:49349007..49352698-chr12:49523718..49526243,3	K562	blood:
7	chr12:49349516..49351260-chr12:49410887..49413470,2	K562	blood:
8	chr12:49349745..49351260-chr12:49410630..49412387,2	K562	blood:
9	chr12:49317412..49320697-chr12:49349793..49352537,4	MCF-7	breast:
10	chr12:49244090..49248564-chr12:49349147..49352476,5	MCF-7	breast:
11	chr12:49348867..49353149-chr12:49362475..49369316,15	MCF-7	breast:
12	chr12:49258480..49261342-chr12:49348804..49351192,2	MCF-7	breast:
13	chr12:49258205..49260442-chr12:49349875..49351715,2	MCF-7	breast:
14	chr12:49244315..49247663-chr12:49350223..49353820,7	MCF-7	breast:
15	chr12:49349743..49353633-chr12:49353636..49360057,10	MCF-7	breast:
16	chr12:49348804..49352502-chr12:49411258..49414497,4	MCF-7	breast:
17	chr12:49347357..49351835-chr12:49360389..49366684,9	MCF-7	breast:
18	chr12:49350125..49350994-chr12:49961421..49962193,2	Hela-S3	cervix:
19	chr12:49208085..49208595-chr12:49350377..49351027,2	K562	blood:
20	chr12:49349770..49352703-chr12:49396550..49398736,3	K562	blood:
21	chr12:49349495..49352296-chr12:49353463..49356229,4	K562	blood:

Variant related genes	Relation type
ARF3	TF binding region
ENSG00000181929	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000238395	Chromatin interaction
ENSG00000255863	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000257913	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000169884	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000181418	Chromatin interaction
ENSG00000134285	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs7981004	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs833826	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs833830	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs833833	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs863855	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 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	chr12:49348000-49350800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr12:49348000-49352200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:49348400-49351000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:49349200-49352000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:49349600-49350600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr12:49349600-49350600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr12:49349600-49350600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr12:49349600-49350600	Flanking Active TSS	Fetal Heart	heart
9	chr12:49349600-49350600	Flanking Active TSS	Dnd41	blood
10	chr12:49349600-49350800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr12:49349600-49351000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr12:49349600-49351000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:49349600-49351800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:49349600-49351800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:49349600-49352000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr12:49349800-49350600	Flanking Active TSS	Fetal Thymus	thymus
17	chr12:49349800-49350600	Flanking Active TSS	Pancreas	Pancrea
18	chr12:49349800-49350800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr12:49349800-49350800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:49349800-49350800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:49349800-49350800	Flanking Active TSS	Liver	Liver
22	chr12:49349800-49351000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr12:49349800-49351000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr12:49349800-49351000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr12:49349800-49351000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr12:49349800-49351400	Active TSS	Placenta Amnion	Placenta Amnion
27	chr12:49349800-49351600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr12:49349800-49351600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:49349800-49351600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:49349800-49352000	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr12:49350000-49350600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:49350000-49350800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr12:49350000-49350800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:49350000-49350800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:49350000-49351000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr12:49350000-49351000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:49350000-49351400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:49350000-49351600	Active TSS	H1 Cell Line	embryonic stem cell
39	chr12:49350000-49351600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:49350000-49351600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:49350000-49351600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:49350000-49351600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:49350000-49351600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:49350000-49351600	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr12:49350000-49351600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:49350000-49351600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:49350000-49351600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:49350000-49351600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr12:49350000-49351600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:49350000-49351600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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