Variant report

Variant	rs12691769
Chromosome Location	chr2:148601538-148601539
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	chr2:148601284-148602455	HepG2	liver:	n/a	n/a
2	CTCF	chr2:148601457-148601626	GM13977	blood:	n/a	n/a
3	MYC	chr2:148601246-148602656	MCF10A-Er-Src	breast:	n/a	n/a
4	CTCF	chr2:148601415-148601649	Fibrobl	skin:	n/a	n/a
5	TAF1	chr2:148601372-148602480	HepG2	liver:	n/a	n/a
6	YY1	chr2:148601473-148602501	GM12892	blood:	n/a	chr2:148602319-148602330 chr2:148602325-148602339 chr2:148602339-148602348 chr2:148602330-148602341 chr2:148602334-148602348 chr2:148602321-148602335 chr2:148602331-148602345 chr2:148602017-148602028
7	RUNX3	chr2:148601241-148602539	GM12878	blood:	n/a	n/a
8	RAD21	chr2:148601383-148601611	GM12878	blood:	n/a	n/a
9	REST	chr2:148600840-148605989	H1-neurons	neurons:	n/a	chr2:148601480-148601493 chr2:148603066-148603073
10	CTCF	chr2:148601460-148601610	HRPEpiC	eye:	n/a	n/a
11	POLR2A	chr2:148600929-148603195	HepG2	liver:	n/a	n/a
12	CTCF	chr2:148601500-148601650	GM12871	blood:	n/a	n/a
13	HNF4A	chr2:148601304-148602487	HepG2	liver:	n/a	n/a
14	MTA3	chr2:148601138-148601862	GM12878	blood:	n/a	n/a
15	RAD21	chr2:148601210-148601798	IMR90	lung:	n/a	n/a
16	MAX	chr2:148600990-148602550	HepG2	liver:	n/a	n/a
17	TBP	chr2:148601071-148602565	HepG2	liver:	n/a	chr2:148601120-148601131
18	POLR2A	chr2:148601108-148601932	HUVEC	blood vessel:	n/a	n/a
19	CTCF	chr2:148601460-148601610	HCPEpiC	choroid plexus:	n/a	n/a
20	MAX	chr2:148601318-148601916	A549	lung:	n/a	n/a
21	POLR2A	chr2:148601434-148602477	GM19193	blood:	n/a	n/a
22	POLR2A	chr2:148601418-148602478	MCF-7	breast:	n/a	n/a
23	CTCF	chr2:148601425-148601633	NHEK	skin:	n/a	n/a
24	POLR2A	chr2:148601500-148602183	PFSK-1	brain:	n/a	n/a
25	CTCF	chr2:148601494-148601635	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr2:148601048-148602584	IMR90	lung:	n/a	n/a
27	POLR2A	chr2:148601413-148602186	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:148601101-148602452	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr2:148601169-148601935	HepG2	liver:	n/a	n/a
30	TAF1	chr2:148601258-148602473	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr2:148601304-148602548	HepG2	liver:	n/a	n/a
32	TBP	chr2:148601415-148602464	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr2:148601228-148602407	Gliobla	brain:	n/a	n/a
34	CTCF	chr2:148601420-148601570	GM06990	blood:	n/a	n/a
35	MBD4	chr2:148600870-148601543	HepG2	liver:	n/a	n/a
36	CTCF	chr2:148601480-148601630	HPAF	blood vessel:	n/a	n/a
37	CTCF	chr2:148601430-148601641	ProgFib	skin:	n/a	n/a
38	CREB1	chr2:148601291-148601951	A549	lung:	n/a	n/a
39	CTCF	chr2:148601420-148601570	HUVEC	blood vessel:	n/a	n/a
40	RAD21	chr2:148601216-148601708	HepG2	liver:	n/a	n/a
41	ZBTB33	chr2:148601523-148602005	HCT-116	colon:	n/a	chr2:148601786-148601801
42	CTCF	chr2:148601440-148601590	GM12867	blood:	n/a	n/a
43	MAX	chr2:148601103-148602516	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr2:148601296-148601964	SK-N-SH	brain:	n/a	n/a
45	CTCF	chr2:148601500-148601650	K562	blood:	n/a	n/a
46	CTCF	chr2:148601460-148601610	GM12866	blood:	n/a	n/a
47	POLR2A	chr2:148601323-148602516	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr2:148601480-148601630	GM12865	blood:	n/a	n/a
49	CTCF	chr2:148601460-148601610	GM12875	blood:	n/a	n/a
50	SP1	chr2:148601483-148602475	HCT-116	colon:	n/a	chr2:148601781-148601788 chr2:148602062-148602074 chr2:148602064-148602073 chr2:148602062-148602074 chr2:148602063-148602072

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:148567317..148569523-chr2:148600689..148602415,2	MCF-7	breast:
2	chr2:148600187..148601857-chr2:148665482..148668201,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ORC4-2	chr2:148600791-148601664	NONHSAT074859

Variant related genes	Relation type
ACVR2A	TF binding region
ENSG00000229143	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10171288	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1156512	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12052736	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12373797	0.89[AMR][1000 genomes]
rs1424943	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1424950	0.89[AFR][1000 genomes]
rs1465486	0.89[AFR][1000 genomes]
rs2081400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2627028	0.89[AMR][1000 genomes]
rs4972315	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6711374	1.00[AMR][1000 genomes]
rs6740168	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv3426833	chr2:148600907-148603455	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3446571	chr2:148601082-148603305	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr2:148600400-148601600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:148600400-148604400	Active TSS	Stomach Smooth Muscle	stomach
3	chr2:148600400-148606200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:148600600-148603800	Active TSS	Brain Anterior Caudate	brain
5	chr2:148600600-148604600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:148600600-148604600	Active TSS	Fetal Brain Female	brain
7	chr2:148600600-148605800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr2:148600600-148606200	Active TSS	HSMMtube	muscle
9	chr2:148600800-148601600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr2:148600800-148601600	Bivalent/Poised TSS	GM12878-XiMat	blood
11	chr2:148600800-148601800	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr2:148600800-148601800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:148600800-148603600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:148600800-148603600	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr2:148600800-148603800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr2:148600800-148603800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:148600800-148603800	Active TSS	Fetal Muscle Leg	muscle
18	chr2:148600800-148604000	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr2:148600800-148604000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:148600800-148604200	Active TSS	H1 Cell Line	embryonic stem cell
21	chr2:148600800-148604200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:148600800-148604200	Active TSS	HSMM	muscle
23	chr2:148600800-148604400	Active TSS	Fetal Stomach	stomach
24	chr2:148600800-148604400	Active TSS	Ovary	ovary
25	chr2:148600800-148604600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:148600800-148604600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:148600800-148604800	Active TSS	Right Atrium	heart
28	chr2:148600800-148605000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:148601000-148601600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr2:148601000-148601800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:148601000-148602200	Bivalent/Poised TSS	Thymus	Thymus
32	chr2:148601000-148603200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:148601000-148603600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:148601000-148603600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:148601000-148603600	Active TSS	Aorta	Aorta
36	chr2:148601000-148603800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:148601000-148604000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:148601000-148604200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:148601000-148604200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr2:148601000-148604200	Active TSS	Left Ventricle	heart
41	chr2:148601000-148604200	Active TSS	Lung	lung
42	chr2:148601000-148604200	Active TSS	Psoas Muscle	Psoas
43	chr2:148601000-148604200	Active TSS	Right Ventricle	heart
44	chr2:148601000-148604400	Active TSS	H9 Cell Line	embryonic stem cell
45	chr2:148601000-148604400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:148601000-148604400	Active TSS	Esophagus	oesophagus
47	chr2:148601000-148604400	Active TSS	Pancreas	Pancrea
48	chr2:148601000-148604400	Active TSS	Rectal Smooth Muscle	rectum
49	chr2:148601000-148604600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:148601000-148604600	Active TSS	Fetal Muscle Trunk	muscle

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