Variant report

Variant	rs833825
Chromosome Location	chr12:49351390-49351391
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	MYC	chr12:49351194-49351412	MCF-7	breast:	n/a	n/a
2	SP1	chr12:49351105-49351495	GM12878	blood:	n/a	chr12:49351277-49351287 chr12:49351278-49351287 chr12:49351277-49351291
3	REST	chr12:49350826-49351622	A549	lung:	n/a	chr12:49351277-49351290
4	NR3C1	chr12:49351199-49351461	A549	lung:	n/a	chr12:49351348-49351357
5	MAX	chr12:49351117-49351439	K562	blood:	n/a	n/a
6	MYC	chr12:49350399-49351491	NB4	blood:	n/a	chr12:49350980-49350989
7	MAX	chr12:49351116-49351507	GM12878	blood:	n/a	n/a
8	MYC	chr12:49351225-49351412	HepG2	liver:	n/a	n/a
9	YY1	chr12:49350888-49351614	HepG2	liver:	n/a	chr12:49350917-49350928 chr12:49351369-49351383 chr12:49351356-49351376
10	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
11	GABPA	chr12:49350840-49351568	A549	lung:	n/a	n/a
12	POLR2A	chr12:49350993-49351655	U87	brain:	n/a	n/a
13	MAX	chr12:49351039-49351643	Hela-S3	cervix:	n/a	n/a
14	GTF2F1	chr12:49351168-49351492	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZBTB33	chr12:49350997-49351617	HepG2	liver:	n/a	chr12:49351310-49351325 chr12:49351348-49351357 chr12:49350999-49351009 chr12:49351346-49351356 chr12:49351343-49351358 chr12:49351349-49351359
16	FOSL2	chr12:49350309-49351465	A549	lung:	n/a	n/a
17	SIN3AK20	chr12:49351042-49351501	PFSK-1	brain:	n/a	n/a
18	MAX	chr12:49349758-49351771	ECC-1	luminal epithelium:	n/a	chr12:49350980-49350989
19	CCNT2	chr12:49350452-49351597	K562	blood:	n/a	chr12:49351278-49351287 chr12:49350593-49350602 chr12:49350880-49350889 chr12:49350886-49350895 chr12:49350626-49350635
20	RCOR1	chr12:49350019-49351660	K562	blood:	n/a	n/a
21	CEBPD	chr12:49351002-49351528	HepG2	liver:	n/a	n/a
22	MAZ	chr12:49350996-49351648	HepG2	liver:	n/a	n/a
23	TAF1	chr12:49350155-49351699	ECC-1	luminal epithelium:	n/a	n/a
24	TAF1	chr12:49350740-49351711	H1-hESC	embryonic stem cell:	n/a	n/a
25	RCOR1	chr12:49351126-49351782	Hela-S3	cervix:	n/a	n/a
26	SIN3AK20	chr12:49350988-49351450	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr12:49350954-49351447	HepG2	liver:	n/a	n/a
28	HEY1	chr12:49350980-49351427	K562	blood:	n/a	n/a
29	SMC3	chr12:49351196-49351502	Hela-S3	cervix:	n/a	n/a
30	TAF1	chr12:49350721-49351429	HepG2	liver:	n/a	n/a
31	ELF1	chr12:49350935-49351620	GM12878	blood:	n/a	chr12:49350992-49351004
32	ELF1	chr12:49349738-49351783	MCF-7	breast:	n/a	chr12:49350992-49351004
33	BCL3	chr12:49350688-49351622	A549	lung:	n/a	chr12:49351563-49351576 chr12:49351278-49351291 chr12:49351369-49351382
34	CTCF	chr12:49350642-49351516	K562	blood:	n/a	n/a
35	POLR2A	chr12:49350189-49351743	U87	brain:	n/a	n/a
36	YY1	chr12:49350943-49351538	GM12878	blood:	n/a	chr12:49351369-49351383 chr12:49351356-49351376
37	MXI1	chr12:49351057-49351713	H1-hESC	embryonic stem cell:	n/a	n/a
38	TCF12	chr12:49350059-49351854	ECC-1	luminal epithelium:	n/a	chr12:49351515-49351523
39	POLR2A	chr12:49351009-49351583	H1-hESC	embryonic stem cell:	n/a	n/a
40	ZBTB33	chr12:49350974-49351635	GM12878	blood:	n/a	chr12:49351310-49351325 chr12:49351348-49351357 chr12:49350999-49351009 chr12:49351346-49351356 chr12:49351343-49351358 chr12:49351349-49351359
41	POLR2A	chr12:49350175-49351738	HUVEC	blood vessel:	n/a	n/a
42	EP300	chr12:49351154-49351493	SK-N-SH_RA	brain:	n/a	n/a
43	FOXP2	chr12:49351050-49351550	PFSK-1	brain:	n/a	n/a
44	ZBTB33	chr12:49350992-49351572	GM12878	blood:	n/a	chr12:49351310-49351325 chr12:49351348-49351357 chr12:49350999-49351009 chr12:49351346-49351356 chr12:49351343-49351358 chr12:49351349-49351359
45	POLR2A	chr12:49350907-49351603	GM18505	blood:	n/a	n/a
46	POLR2A	chr12:49350935-49351600	SK-N-SH	brain:	n/a	n/a
47	GABPA	chr12:49351058-49351399	HepG2	liver:	n/a	n/a
48	POLR2A	chr12:49350041-49351803	H1-neurons	neurons:	n/a	n/a
49	POLR2A	chr12:49350898-49351561	GM19193	blood:	n/a	n/a
50	POLR2A	chr12:49350854-49351566	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49349835..49352133-chr12:49390670..49393580,2	K562	blood:
2	chr12:49326822..49334011-chr12:49345841..49353556,12	MCF-7	breast:
3	chr12:49349202..49351999-chr12:49410599..49414055,4	MCF-7	breast:
4	chr12:49349007..49352698-chr12:49523718..49526243,3	K562	blood:
5	chr12:49350460..49352797-chr12:49389222..49392992,4	MCF-7	breast:
6	chr12:49317412..49320697-chr12:49349793..49352537,4	MCF-7	breast:
7	chr12:49244090..49248564-chr12:49349147..49352476,5	MCF-7	breast:
8	chr12:49348867..49353149-chr12:49362475..49369316,15	MCF-7	breast:
9	chr12:49258205..49260442-chr12:49349875..49351715,2	MCF-7	breast:
10	chr12:49244315..49247663-chr12:49350223..49353820,7	MCF-7	breast:
11	chr12:49349743..49353633-chr12:49353636..49360057,10	MCF-7	breast:
12	chr12:49348804..49352502-chr12:49411258..49414497,4	MCF-7	breast:
13	chr12:49347357..49351835-chr12:49360389..49366684,9	MCF-7	breast:
14	chr12:49351134..49353553-chr12:49353996..49358640,5	MCF-7	breast:
15	chr12:49349770..49352703-chr12:49396550..49398736,3	K562	blood:
16	chr12:49351084..49352752-chr12:49363357..49365742,2	K562	blood:
17	chr12:49349495..49352296-chr12:49353463..49356229,4	K562	blood:

Variant related genes	Relation type
ARF3	TF binding region
ENSG00000272822	TF binding region
ENSG00000134285	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000238395	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000181418	Chromatin interaction
ENSG00000257913	Chromatin interaction
ENSG00000169884	Chromatin interaction
ENSG00000255863	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000258017	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11168810	0.84[AFR][1000 genomes]
rs12122	0.88[AMR][1000 genomes]
rs2694841	0.88[AMR][1000 genomes]
rs708242	0.88[AMR][1000 genomes]
rs833823	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs833829	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs833834	0.82[AFR][1000 genomes]
rs833835	0.82[AFR][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	chr12:49348000-49352200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:49349200-49352000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:49349600-49351800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:49349600-49351800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:49349600-49352000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr12:49349800-49351400	Active TSS	Placenta Amnion	Placenta Amnion
7	chr12:49349800-49351600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr12:49349800-49351600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:49349800-49351600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:49349800-49352000	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr12:49350000-49351400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:49350000-49351600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr12:49350000-49351600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:49350000-49351600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:49350000-49351600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:49350000-49351600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:49350000-49351600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:49350000-49351600	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr12:49350000-49351600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:49350000-49351600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:49350000-49351600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:49350000-49351600	Active TSS	Muscle Satellite Cultured Cells	--
23	chr12:49350000-49351600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:49350000-49351600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:49350000-49351600	Active TSS	Fetal Intestine Large	intestine
26	chr12:49350000-49351600	Active TSS	Fetal Intestine Small	intestine
27	chr12:49350000-49351600	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr12:49350000-49351600	Active TSS	Psoas Muscle	Psoas
29	chr12:49350000-49351600	Active TSS	GM12878-XiMat	blood
30	chr12:49350000-49351600	Active TSS	HSMM	muscle
31	chr12:49350000-49351600	Active TSS	HSMMtube	muscle
32	chr12:49350000-49351600	Active TSS	NH-A	brain
33	chr12:49350000-49351600	Active TSS	NHLF	lung
34	chr12:49350000-49351800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr12:49350000-49351800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:49350000-49351800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:49350000-49351800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr12:49350000-49351800	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr12:49350000-49351800	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr12:49350000-49351800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr12:49350000-49351800	Active TSS	Aorta	Aorta
42	chr12:49350000-49351800	Active TSS	NHDF-Ad	bronchial
43	chr12:49350000-49352000	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr12:49350000-49352000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:49350000-49352200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:49350000-49352200	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr12:49350200-49351400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:49350200-49351400	Active TSS	Brain Substantia Nigra	brain
49	chr12:49350200-49351400	Active TSS	Esophagus	oesophagus
50	chr12:49350200-49351400	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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