Variant report

Variant	rs3809143
Chromosome Location	chr12:122232580-122232581
allele	A/C
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	POLR2A	chr12:122232008-122233687	K562	blood:	n/a	n/a
2	POLR2A	chr12:122231913-122233948	GM12891	blood:	n/a	n/a
3	CTCF	chr12:122231696-122233281	K562	blood:	n/a	chr12:122233004-122233014 chr12:122232237-122232255 chr12:122232310-122232328 chr12:122232999-122233017 chr12:122232322-122232335 chr12:122233001-122233022 chr12:122232312-122232325 chr12:122233002-122233015 chr12:122233000-122233016 chr12:122232299-122232308 chr12:122233002-122233011
4	MXI1	chr12:122231965-122232614	H1-hESC	embryonic stem cell:	n/a	n/a
5	SMC3	chr12:122231392-122233304	Hela-S3	cervix:	n/a	chr12:122232687-122232697 chr12:122233001-122233015
6	BCL3	chr12:122231462-122233359	A549	lung:	n/a	chr12:122231561-122231570 chr12:122232267-122232280
7	POLR2A	chr12:122231942-122234684	K562	blood:	n/a	n/a
8	POLR2A	chr12:122232576-122232775	A549	lung:	n/a	n/a
9	USF1	chr12:122231591-122232653	A549	lung:	n/a	chr12:122232264-122232280 chr12:122232263-122232279
10	POLR2A	chr12:122229405-122233468	GM19099	blood:	n/a	n/a
11	POLR2A	chr12:122231256-122234731	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr12:122231734-122233484	K562	blood:	n/a	n/a
13	MYC	chr12:122231706-122233218	K562	blood:	n/a	chr12:122231986-122231996
14	POLR2A	chr12:122231155-122237092	GM12892	blood:	n/a	n/a
15	POLR2A	chr12:122231853-122233037	ProgFib	skin:	n/a	n/a
16	POLR2A	chr12:122231262-122233824	GM12891	blood:	n/a	n/a
17	MAX	chr12:122231795-122232631	MCF-7	breast:	n/a	chr12:122231986-122231996
18	POLR2A	chr12:122231991-122233867	GM12891	blood:	n/a	n/a
19	POLR2A	chr12:122231952-122233279	HepG2	liver:	n/a	n/a
20	POLR2A	chr12:122231286-122233689	A549	lung:	n/a	n/a
21	EP300	chr12:122231852-122232617	GM12878	blood:	n/a	chr12:122232266-122232275 chr12:122232263-122232272
22	NRF1	chr12:122231994-122232585	GM12878	blood:	n/a	n/a
23	MYC	chr12:122232134-122232612	HUVEC	blood vessel:	n/a	n/a
24	SIN3AK20	chr12:122230934-122233186	PANC-1	pancreas:	n/a	n/a
25	MYC	chr12:122231409-122233174	A549	lung:	n/a	chr12:122231986-122231996 chr12:122231622-122231632
26	EP300	chr12:122232283-122232621	K562	blood:	n/a	n/a
27	GABPA	chr12:122232006-122232595	MCF-7	breast:	n/a	n/a
28	POLR2A	chr12:122231910-122233704	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:122231318-122233921	HepG2	liver:	n/a	n/a
30	MTA3	chr12:122229860-122233383	GM12878	blood:	n/a	n/a
31	CTCF	chr12:122231535-122233389	MCF-7	breast:	n/a	chr12:122233004-122233014 chr12:122232237-122232255 chr12:122232310-122232328 chr12:122232999-122233017 chr12:122232322-122232335 chr12:122233001-122233022 chr12:122232312-122232325 chr12:122233002-122233015 chr12:122233000-122233016 chr12:122232299-122232308 chr12:122233002-122233011
32	POLR2A	chr12:122229522-122241538	HepG2	liver:	n/a	n/a
33	BCL3	chr12:122229500-122233523	A549	lung:	n/a	chr12:122231001-122231010 chr12:122229915-122229923 chr12:122231561-122231570 chr12:122231384-122231397 chr12:122232267-122232280 chr12:122231383-122231396
34	TCF12	chr12:122231569-122232673	ECC-1	luminal epithelium:	n/a	chr12:122231871-122231881 chr12:122232576-122232586
35	POLR2A	chr12:122232041-122233290	SK-N-SH	brain:	n/a	n/a
36	PAX5	chr12:122231388-122232654	GM12878	blood:	n/a	n/a
37	CBX3	chr12:122231492-122233287	K562	blood:	n/a	n/a
38	CTCF	chr12:122231422-122233430	HCT-116	colon:	n/a	chr12:122233004-122233014 chr12:122232237-122232255 chr12:122232310-122232328 chr12:122232999-122233017 chr12:122232322-122232335 chr12:122233001-122233022 chr12:122232312-122232325 chr12:122233002-122233015 chr12:122233000-122233016 chr12:122232299-122232308 chr12:122233002-122233011
39	CTCF	chr12:122232575-122232625	HepG2	liver:	n/a	n/a
40	POLR2A	chr12:122230693-122233942	HepG2	liver:	n/a	n/a
41	E2F6	chr12:122231636-122232606	A549	lung:	n/a	chr12:122231916-122231925
42	BHLHE40	chr12:122232006-122233169	K562	blood:	n/a	chr12:122232264-122232280 chr12:122232263-122232279
43	POLR2A	chr12:122232014-122233778	GM12892	blood:	n/a	n/a
44	CTCF	chr12:122231674-122233365	K562	blood:	n/a	chr12:122233004-122233014 chr12:122232237-122232255 chr12:122232310-122232328 chr12:122232999-122233017 chr12:122232322-122232335 chr12:122233001-122233022 chr12:122232312-122232325 chr12:122233002-122233015 chr12:122233000-122233016 chr12:122232299-122232308 chr12:122233002-122233011
45	CTCF	chr12:122231945-122232682	HepG2	liver:	n/a	chr12:122232237-122232255 chr12:122232310-122232328 chr12:122232322-122232335 chr12:122232312-122232325 chr12:122232299-122232308
46	CEBPB	chr12:122232079-122232582	K562	blood:	n/a	n/a
47	POU2F2	chr12:122231780-122232895	GM12891	blood:	n/a	chr12:122232602-122232614
48	E2F6	chr12:122231442-122233187	A549	lung:	n/a	chr12:122231598-122231607 chr12:122231563-122231572 chr12:122231916-122231925
49	MAZ	chr12:122230686-122233217	GM12878	blood:	n/a	chr12:122231986-122231996 chr12:122231622-122231632
50	PBX3	chr12:122231574-122233350	SK-N-SH	brain:	n/a	chr12:122231915-122231924

No.	Distal block	Cell Line	Cell type
1	chr12:122213783..122214655-chr12:122231473..122233403,7	MCF-7	breast:
2	chr12:122232516..122233068-chr12:122251132..122251938,2	MCF-7	breast:
3	chr12:122231775..122233087-chr12:122326346..122327350,5	MCF-7	breast:
4	chr12:122230934..122233822-chr12:122459500..122463009,3	MCF-7	breast:
5	chr12:122213768..122214693-chr12:122231771..122233483,12	K562	blood:
6	chr12:122232032..122233517-chr12:122325701..122326925,10	MCF-7	breast:
7	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
8	chr12:122214138..122216054-chr12:122231373..122233377,2	K562	blood:
9	chr12:122232031..122232725-chr12:122326601..122327197,2	MCF-7	breast:
10	chr12:122231812..122233476-chr12:122325996..122327591,21	K562	blood:
11	chr12:122213296..122215371-chr12:122231546..122233202,23	MCF-7	breast:
12	chr12:121974972..121977558-chr12:122231894..122235040,4	MCF-7	breast:
13	chr12:121836495..121838050-chr12:122231938..122234187,2	K562	blood:
14	chr12:122149249..122152147-chr12:122229581..122233327,7	MCF-7	breast:
15	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
16	chr1:116445666..116447671-chr12:122232460..122234006,2	MCF-7	breast:
17	chr12:122232296..122232847-chr12:122332552..122333272,2	MCF-7	breast:
18	chr12:122232180..122234901-chr12:122344222..122346588,2	K562	blood:
19	chr12:116997056..116999076-chr12:122230249..122232872,2	K562	blood:
20	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
21	chr12:122232294..122232984-chr12:122241949..122242571,2	K562	blood:
22	chr12:122188669..122193873-chr12:122227176..122233304,8	MCF-7	breast:
23	chr12:122017334..122020292-chr12:122231782..122234542,4	K562	blood:
24	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272849	TF binding region
RHOF	TF binding region
ENSG00000139718	Chromatin interaction
ENSG00000256742	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000089053	Chromatin interaction
ENSG00000171471	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000170633	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000239082	Chromatin interaction
ENSG00000256950	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17522849	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36023382	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3741594	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58801491	1.00[ASN][1000 genomes]
rs59126522	0.90[AFR][1000 genomes]
rs59912940	0.93[ASN][1000 genomes]
rs61736010	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61743641	0.83[EUR][1000 genomes];1.00[ASN][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 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	chr12:122225800-122233200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr12:122229400-122233000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:122229400-122233000	Flanking Active TSS	Duodenum Mucosa	Duodenum
4	chr12:122229600-122235400	Enhancers	Fetal Heart	heart
5	chr12:122229800-122233000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:122230000-122233200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr12:122230200-122233000	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr12:122230200-122233000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
9	chr12:122230400-122232800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:122230600-122232600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:122230600-122232800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr12:122230600-122233000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr12:122230600-122233200	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr12:122230600-122233400	Flanking Active TSS	Dnd41	blood
15	chr12:122230800-122232600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:122230800-122232600	Flanking Active TSS	Fetal Thymus	thymus
17	chr12:122230800-122233000	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:122230800-122236400	Enhancers	Fetal Brain Male	brain
19	chr12:122231000-122233000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr12:122231200-122232600	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr12:122231200-122232600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr12:122231200-122232600	Active TSS	Psoas Muscle	Psoas
23	chr12:122231200-122232800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:122231200-122233000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:122231200-122233000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:122231200-122233200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:122231400-122232600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr12:122231400-122232800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:122231400-122233000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr12:122231400-122233000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr12:122231400-122233000	Flanking Active TSS	Pancreas	Pancrea
32	chr12:122231400-122233200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr12:122231400-122233400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr12:122231400-122233600	Flanking Active TSS	Liver	Liver
35	chr12:122231400-122233800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr12:122231400-122235000	Flanking Active TSS	HepG2	liver
37	chr12:122231600-122232800	Active TSS	Aorta	Aorta
38	chr12:122231600-122232800	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr12:122231600-122232800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr12:122231600-122233000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr12:122231600-122233000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:122231600-122233000	Flanking Active TSS	Osteobl	bone
43	chr12:122231600-122233200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr12:122231600-122233200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:122231800-122232600	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr12:122231800-122232800	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr12:122231800-122233000	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr12:122231800-122233000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:122231800-122233000	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr12:122231800-122233200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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