Variant report

Variant	rs12829785
Chromosome Location	chr12:62860794-62860795
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	POLR2A	chr12:62859874-62861015	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr12:62860120-62861114	PFSK-1	brain:	n/a	n/a
3	CTCF	chr12:62860660-62860810	RPTEC	kidney:	n/a	n/a
4	POLR2A	chr12:62859881-62861326	MCF10A-Er-Src	breast:	n/a	n/a
5	CREB1	chr12:62860144-62861212	GM12878	blood:	n/a	chr12:62860570-62860583 chr12:62861108-62861121
6	CHD1	chr12:62860398-62861339	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:62859869-62861155	GM18951	blood:	n/a	n/a
8	POLR2A	chr12:62860181-62860863	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr12:62860097-62861390	HepG2	liver:	n/a	n/a
10	ELF1	chr12:62860290-62860814	A549	lung:	n/a	chr12:62860557-62860568 chr12:62860581-62860590 chr12:62860703-62860712 chr12:62860557-62860568 chr12:62860555-62860568 chr12:62860558-62860567
11	ELF1	chr12:62860242-62861043	HepG2	liver:	n/a	chr12:62860557-62860568 chr12:62860581-62860590 chr12:62860703-62860712 chr12:62860557-62860568 chr12:62860555-62860568 chr12:62860558-62860567
12	GABPA	chr12:62860362-62860888	H1-hESC	embryonic stem cell:	n/a	n/a
13	RCOR1	chr12:62859535-62861130	K562	blood:	n/a	n/a
14	CTCF	chr12:62860731-62860848	GM19240	blood:	n/a	n/a
15	RCOR1	chr12:62860219-62861144	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:62860158-62861006	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:62860146-62860995	GM12892	blood:	n/a	n/a
18	TAF1	chr12:62860432-62860807	GM12891	blood:	n/a	n/a
19	MYC	chr12:62859916-62861021	NB4	blood:	n/a	n/a
20	MAX	chr12:62859863-62861263	ECC-1	luminal epithelium:	n/a	n/a
21	GATA3	chr12:62860252-62860830	T-47D	breast:	n/a	n/a
22	POLR2A	chr12:62860269-62861007	Gliobla	brain:	n/a	n/a
23	GABPA	chr12:62859931-62861228	A549	lung:	n/a	n/a
24	RFX5	chr12:62859899-62861293	Hela-S3	cervix:	n/a	n/a
25	ETS1	chr12:62860285-62860877	K562	blood:	n/a	chr12:62860560-62860570 chr12:62860559-62860570 chr12:62860559-62860568 chr12:62860559-62860568
26	CHD2	chr12:62860173-62861153	H1-hESC	embryonic stem cell:	n/a	n/a
27	YY1	chr12:62860356-62860923	H1-hESC	embryonic stem cell:	n/a	chr12:62860502-62860516 chr12:62860704-62860715 chr12:62860468-62860479 chr12:62860531-62860540
28	GABPA	chr12:62860004-62860983	SK-N-SH	brain:	n/a	n/a
29	YY1	chr12:62860286-62860875	SK-N-SH_RA	brain:	n/a	chr12:62860502-62860516 chr12:62860704-62860715 chr12:62860468-62860479 chr12:62860531-62860540
30	GABPA	chr12:62860154-62860884	A549	lung:	n/a	n/a
31	HMGN3	chr12:62860327-62860987	K562	blood:	n/a	n/a
32	YY1	chr12:62860304-62861241	GM12878	blood:	n/a	chr12:62860502-62860516 chr12:62860704-62860715 chr12:62860468-62860479 chr12:62860531-62860540
33	POLR2A	chr12:62860099-62861208	GM12878	blood:	n/a	n/a
34	MYC	chr12:62860376-62860806	MCF-7	breast:	n/a	n/a
35	FOXM1	chr12:62860232-62860932	GM12878	blood:	n/a	n/a
36	PAX5	chr12:62860408-62860819	GM12892	blood:	n/a	n/a
37	GTF2F1	chr12:62860547-62861389	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr12:62860368-62860943	H1-hESC	embryonic stem cell:	n/a	n/a
39	CREB1	chr12:62860302-62860886	H1-hESC	embryonic stem cell:	n/a	chr12:62860570-62860583
40	ZNF143	chr12:62860356-62861109	GM12878	blood:	n/a	n/a
41	POLR2A	chr12:62860288-62860801	SK-N-SH	brain:	n/a	n/a
42	EP300	chr12:62859927-62860945	K562	blood:	n/a	chr12:62860560-62860567 chr12:62860695-62860711 chr12:62860495-62860511
43	YY1	chr12:62860296-62861206	ECC-1	luminal epithelium:	n/a	chr12:62860502-62860516 chr12:62860704-62860715 chr12:62860468-62860479 chr12:62860531-62860540
44	PML	chr12:62860285-62861299	K562	blood:	n/a	chr12:62860892-62860900
45	CTCF	chr12:62860726-62860808	MCF-7	breast:	n/a	n/a
46	POLR2A	chr12:62860183-62861082	K562	blood:	n/a	n/a
47	MYBL2	chr12:62860286-62860858	HepG2	liver:	n/a	n/a
48	BHLHE40	chr12:62860200-62861028	K562	blood:	n/a	chr12:62860697-62860713
49	POLR2A	chr12:62859882-62861034	GM18526	blood:	n/a	n/a
50	CTCF	chr12:62860780-62860930	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:62860780-62860830	GM12891	blood:	n/a
2	chr12:62860780-62860830	IMR90	lung:	fetal
3	chr12:62860780-62860830	A549	lung:	n/a
4	chr12:62860780-62860830	AG04450	lung:	fetal
5	chr12:62860780-62860830	AG10803	skin:	n/a
6	chr12:62860780-62860830	PrEC	prostate:	n/a
7	chr12:62860780-62860830	NB4	blood:	n/a
8	chr12:62860780-62860830	K562	blood:	n/a
9	chr12:62860780-62860830	HCPEpiC	choroid plexus:	n/a
10	chr12:62860780-62860830	H1-hESC	embryonic stem cell:	embryo
11	chr12:62860780-62860830	HPAEpiC	pulmonary alveolar:	n/a
12	chr12:62860780-62860830	Jurkat	blood:	n/a
13	chr12:62860780-62860830	SKMC	muscle:	n/a
14	chr12:62860780-62860830	ECC-1	luminal epithelium:	n/a
15	chr12:62860780-62860830	LNCaP	prostate:	n/a
16	chr12:62860780-62860830	HEEpiC	esophagus:	n/a
17	chr12:62860780-62860830	SK-N-MC	brain:	n/a
18	chr12:62860780-62860830	HEK293	kidney:	embryo
19	chr12:62860780-62860830	SAEC	small airway:	n/a
20	chr12:62860780-62860830	HNPCEpiC	eye:	n/a
21	chr12:62860780-62860830	GM12892	blood:	n/a
22	chr12:62860780-62860830	PFSK-1	brain:	n/a
23	chr12:62860780-62860830	GM12878	blood:	n/a
24	chr12:62860780-62860830	T-47D	breast:	n/a
25	chr12:62860780-62860830	SK-N-SH_RA	brain:	n/a
26	chr12:62860780-62860830	ProgFib	skin:	n/a
27	chr12:62860780-62860830	GM19239	blood:	n/a
28	chr12:62860780-62860830	HMEC	breast:	n/a
29	chr12:62860780-62860830	HRCEpiC	kidney:	n/a
30	chr12:62860780-62860830	NT2-D1	testis:	n/a
31	chr12:62860780-62860830	Hela-S3	cervix:	n/a
32	chr12:62860780-62860830	HIPEpiC	eye:	n/a
33	chr12:62860780-62860830	GM06990	blood:	n/a
34	chr12:62860780-62860830	HRPEpiC	eye:	n/a
35	chr12:62860780-62860830	HCT-116	colon:	n/a
36	chr12:62860780-62860830	MCF10A-Er-Src	breast:	n/a
37	chr12:62860780-62860830	BE2_C	brain:	n/a
38	chr12:62860780-62860830	HCM	heart:	n/a
39	chr12:62860780-62860830	CMK	blood:	n/a
40	chr12:62860780-62860830	NHDF-neo	bronchial:	n/a
41	chr12:62860780-62860830	HepG2	liver:	n/a
42	chr12:62860780-62860830	Caco-2	colon:	n/a
43	chr12:62860780-62860830	MCF-7	breast:	n/a
44	chr12:62860780-62860830	HRE	kidney:	n/a
45	chr12:62860780-62860830	HAEpiC	amniotic membrane:	n/a
46	chr12:62860780-62860830	AG04449	skin:	fetal
47	chr12:62860780-62860830	RPTEC	kidney:	n/a
48	chr12:62860780-62860830	AG09309	skin:	n/a
49	chr12:62860780-62860830	ovcar-3	ovarian:	n/a
50	chr12:62860780-62860830	BJ	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:62859264..62862504-chr12:62994446..62997723,4	K562	blood:
2	chr12:62860603..62862408-chr12:62877064..62881508,4	MCF-7	breast:
3	chr12:62859326..62863326-chr12:62876630..62881311,5	K562	blood:
4	chr12:62652867..62655436-chr12:62859516..62862606,3	MCF-7	breast:
5	chr12:62859286..62861275-chr12:62995759..62997449,2	MCF-7	breast:

Variant related genes	Relation type
MON2	TF binding region
MON2	CpG island
ENSG00000257354	Chromatin interaction
ENSG00000198673	Chromatin interaction
ENSG00000221949	Chromatin interaction
ENSG00000199179	Chromatin interaction
ENSG00000135655	Chromatin interaction
ENSG00000257568	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11174446	1.00[ASW][hapmap]
rs12825098	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35499412	1.00[AFR][1000 genomes]
rs35646256	1.00[AFR][1000 genomes];0.81[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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12829785	MMP20	trans	lymphoblastoid	seeQTL
rs12829785	FCRL2	trans	lymphoblastoid	seeQTL
rs12829785	DBNDD2	trans	lymphoblastoid	seeQTL
rs12829785	GRASP	trans	lymphoblastoid	seeQTL
rs12829785	FGFBP2	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62859400-62861800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr12:62859400-62862600	Active TSS	Duodenum Mucosa	Duodenum
3	chr12:62859400-62863600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:62859600-62861000	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr12:62859600-62861200	Active TSS	Adipose Nuclei	Adipose
6	chr12:62859600-62861200	Active TSS	Brain Anterior Caudate	brain
7	chr12:62859600-62861400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:62859600-62861400	Active TSS	Brain Cingulate Gyrus	brain
9	chr12:62859600-62861400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:62859600-62861400	Active TSS	Fetal Brain Male	brain
11	chr12:62859600-62861400	Active TSS	Fetal Kidney	kidney
12	chr12:62859600-62861400	Active TSS	Fetal Lung	lung
13	chr12:62859600-62861400	Active TSS	Thymus	Thymus
14	chr12:62859600-62861600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:62859600-62861600	Active TSS	Brain Angular Gyrus	brain
16	chr12:62859600-62861600	Active TSS	Brain Substantia Nigra	brain
17	chr12:62859600-62861600	Active TSS	Fetal Muscle Leg	muscle
18	chr12:62859600-62861800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr12:62859600-62862000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:62859600-62862000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:62859600-62862000	Active TSS	Fetal Muscle Trunk	muscle
22	chr12:62859600-62862200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:62859600-62862200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:62859600-62862200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:62859600-62862200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:62859600-62862200	Active TSS	Aorta	Aorta
27	chr12:62859600-62862200	Active TSS	Right Ventricle	heart
28	chr12:62859600-62862600	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr12:62859600-62862600	Active TSS	Fetal Intestine Large	intestine
30	chr12:62859600-62862600	Active TSS	Ovary	ovary
31	chr12:62859600-62862600	Active TSS	NH-A	brain
32	chr12:62859600-62863000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:62859600-62863200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:62859600-62863200	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr12:62859800-62861000	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr12:62859800-62861200	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr12:62859800-62861200	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr12:62859800-62861200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:62859800-62861400	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr12:62859800-62861400	Active TSS	Fetal Heart	heart
41	chr12:62859800-62861600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:62859800-62861600	Active TSS	Esophagus	oesophagus
43	chr12:62859800-62861600	Active TSS	Rectal Smooth Muscle	rectum
44	chr12:62859800-62861800	Active TSS	H1 Cell Line	embryonic stem cell
45	chr12:62859800-62861800	Active TSS	H9 Cell Line	embryonic stem cell
46	chr12:62859800-62861800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:62859800-62861800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:62859800-62861800	Active TSS	Colonic Mucosa	Colon
49	chr12:62859800-62861800	Active TSS	Psoas Muscle	Psoas
50	chr12:62859800-62861800	Active TSS	HSMMtube	muscle

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