Variant report

Variant	rs1874909
Chromosome Location	chr12:49741936-49741937
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	chr12:49741620-49741979	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr12:49740402-49742031	MCF-7	breast:	n/a	n/a
3	MAX	chr12:49740385-49742027	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr12:49740213-49742052	ECC-1	luminal epithelium:	n/a	chr12:49741032-49741042
5	POLR2A	chr12:49741624-49741988	A549	lung:	n/a	n/a
6	RFX5	chr12:49741606-49741998	HepG2	liver:	n/a	n/a
7	GABPA	chr12:49741448-49741957	A549	lung:	n/a	n/a
8	SP1	chr12:49741262-49742139	A549	lung:	n/a	chr12:49741868-49741882
9	CTCF	chr12:49741840-49741990	GM12869	blood:	n/a	n/a
10	FOSL2	chr12:49740940-49742510	A549	lung:	n/a	chr12:49742311-49742320 chr12:49741845-49741854 chr12:49742312-49742319 chr12:49742311-49742319 chr12:49741670-49741679 chr12:49742307-49742318
11	MAX	chr12:49740435-49742080	A549	lung:	n/a	n/a
12	ZBTB7A	chr12:49738646-49742163	ECC-1	luminal epithelium:	n/a	chr12:49739274-49739281 chr12:49741924-49741935 chr12:49741555-49741564
13	EGR1	chr12:49741176-49741951	HCT-116	colon:	n/a	chr12:49741709-49741719
14	MBD4	chr12:49741344-49741953	HepG2	liver:	n/a	n/a
15	ELF1	chr12:49741427-49741942	HepG2	liver:	n/a	chr12:49741594-49741606 chr12:49741549-49741558
16	CTCF	chr12:49740978-49741984	HCT-116	colon:	n/a	chr12:49741554-49741572 chr12:49741549-49741570 chr12:49741555-49741571 chr12:49741556-49741569 chr12:49741556-49741569
17	SP1	chr12:49741156-49742136	A549	lung:	n/a	chr12:49741189-49741202 chr12:49741868-49741882
18	POLR2A	chr12:49741543-49741978	HepG2	liver:	n/a	n/a
19	TCF12	chr12:49740418-49742001	ECC-1	luminal epithelium:	n/a	chr12:49741032-49741042
20	CTCF	chr12:49741936-49741939	GM19238	blood:	n/a	n/a
21	YY1	chr12:49741344-49742010	HepG2	liver:	n/a	chr12:49741710-49741721 chr12:49741662-49741676 chr12:49741565-49741577 chr12:49741552-49741566
22	YY1	chr12:49741362-49741990	A549	lung:	n/a	chr12:49741710-49741721 chr12:49741662-49741676 chr12:49741565-49741577 chr12:49741552-49741566
23	EP300	chr12:49741306-49742392	A549	lung:	n/a	chr12:49742310-49742319 chr12:49741615-49741631 chr12:49742311-49742320
24	POLR2A	chr12:49741620-49741951	MCF10A-Er-Src	breast:	n/a	n/a
25	REST	chr12:49741010-49742198	A549	lung:	n/a	chr12:49741422-49741442 chr12:49741591-49741604 chr12:49741582-49741595
26	TAF1	chr12:49741383-49742195	A549	lung:	n/a	n/a
27	REST	chr12:49741457-49742012	HepG2	liver:	n/a	chr12:49741591-49741604 chr12:49741582-49741595
28	POLR2A	chr12:49741447-49741986	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr12:49741593-49741973	Gliobla	brain:	n/a	n/a
30	SP1	chr12:49741457-49742025	HepG2	liver:	n/a	chr12:49741868-49741882
31	BRCA1	chr12:49741493-49741952	HepG2	liver:	n/a	n/a
32	POLR2A	chr12:49741455-49742756	HepG2	liver:	n/a	n/a
33	HNF4A	chr12:49741468-49742038	HepG2	liver:	n/a	chr12:49741780-49741792 chr12:49741779-49741793 chr12:49741778-49741793 chr12:49741779-49741794 chr12:49741780-49741792
34	HDAC2	chr12:49740223-49742034	MCF-7	breast:	n/a	n/a
35	SMC3	chr12:49740372-49742164	SK-N-SH	brain:	n/a	chr12:49741556-49741570 chr12:49741556-49741566 chr12:49741019-49741027
36	TAF1	chr12:49741398-49742048	HepG2	liver:	n/a	n/a
37	MBD4	chr12:49741559-49742094	HepG2	liver:	n/a	n/a
38	POLR2A	chr12:49741614-49742040	HepG2	liver:	n/a	n/a
39	POLR2A	chr12:49741512-49742143	MCF-7	breast:	n/a	n/a
40	POLR2A	chr12:49741497-49742083	MCF-7	breast:	n/a	n/a
41	ATF3	chr12:49741310-49742049	A549	lung:	n/a	n/a
42	POLR2A	chr12:49741384-49742095	HCT-116	colon:	n/a	n/a
43	POLR2A	chr12:49741585-49742027	IMR90	lung:	n/a	n/a
44	HNF4G	chr12:49741474-49741988	HepG2	liver:	n/a	chr12:49741780-49741792 chr12:49741779-49741793 chr12:49741779-49741794 chr12:49741780-49741792
45	POLR2A	chr12:49741696-49741940	A549	lung:	n/a	n/a
46	TEAD4	chr12:49741383-49742068	HepG2	liver:	n/a	n/a
47	HDAC2	chr12:49741358-49741956	HepG2	liver:	n/a	n/a
48	SIX5	chr12:49741173-49742180	A549	lung:	n/a	n/a
49	TEAD4	chr12:49741036-49741980	ECC-1	luminal epithelium:	n/a	n/a
50	CTCF	chr12:49740404-49742833	A549	lung:	n/a	chr12:49741554-49741572 chr12:49741549-49741570 chr12:49740510-49740523 chr12:49741555-49741571 chr12:49741556-49741569 chr12:49741556-49741569

No.	Distal block	Cell Line	Cell type
1	chr12:49688782..49690788-chr12:49741064..49743191,2	MCF-7	breast:
2	chr12:49691871..49692482-chr12:49741193..49741985,2	MCF-7	breast:
3	chr12:49656587..49660636-chr12:49733539..49743833,13	K562	blood:
4	chr12:49741030..49742987-chr12:49986875..49988929,2	K562	blood:
5	chr12:49739131..49745064-chr12:49758784..49762517,10	MCF-7	breast:
6	chr12:49683076..49686072-chr12:49740867..49742928,2	MCF-7	breast:
7	chr12:49657182..49662198-chr12:49738070..49742868,13	MCF-7	breast:
8	chr12:49740569..49744952-chr12:49759719..49761508,3	K562	blood:
9	chr12:49740075..49745225-chr12:49756992..49761732,8	K562	blood:
10	chr12:49740266..49744152-chr12:49960185..49963713,4	MCF-7	breast:
11	chr12:49715312..49722303-chr12:49739075..49744198,13	MCF-7	breast:
12	chr12:49741114..49742103-chr12:50016468..50017223,2	K562	blood:
13	chr12:49725094..49726383-chr12:49741023..49741965,3	MCF-7	breast:
14	chr12:49681907..49682823-chr12:49741104..49742122,6	MCF-7	breast:
15	chr12:49725108..49725946-chr12:49741085..49742047,4	K562	blood:
16	chr12:49741847..49743378-chr12:49752889..49755396,2	MCF-7	breast:
17	chr12:49740264..49744957-chr12:49759411..49762039,7	MCF-7	breast:
18	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:
19	chr12:49741089..49742059-chr12:49973951..49974946,3	K562	blood:
20	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
21	chr12:49741446..49744429-chr12:50016284..50018933,2	MCF-7	breast:

Variant related genes	Relation type
DNAJC22	TF binding region
ENSG00000167553	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000258284	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000199237	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000187778	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10506284	0.96[EUR][1000 genomes]
rs10506285	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168981	0.94[ASN][1000 genomes]
rs11831313	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11835071	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12299777	0.87[ASN][1000 genomes]
rs12306866	0.94[ASN][1000 genomes]
rs12310129	0.94[ASN][1000 genomes]
rs12317856	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17123696	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1874910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874911	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270741	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60331259	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60494978	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74089059	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74089062	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089066	0.96[EUR][1000 genomes]
rs7955245	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49738800-49742000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr12:49738800-49742000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr12:49738800-49742000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:49739000-49742000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:49739000-49742000	Enhancers	Lung	lung
6	chr12:49739000-49742200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:49739200-49742000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
8	chr12:49739200-49742200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
9	chr12:49739400-49742000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:49739400-49742000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
11	chr12:49739400-49742000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
12	chr12:49739400-49742000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
13	chr12:49739400-49742200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:49739600-49742400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
15	chr12:49740200-49742000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
16	chr12:49740200-49742200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:49740400-49742000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
18	chr12:49740400-49742000	Enhancers	Spleen	Spleen
19	chr12:49740600-49742000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:49740600-49742000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
21	chr12:49740600-49742200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
22	chr12:49740600-49742200	Flanking Active TSS	Hela-S3	cervix
23	chr12:49740800-49742400	Flanking Active TSS	Pancreas	Pancrea
24	chr12:49741000-49742400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
25	chr12:49741000-49742600	Bivalent Enhancer	Fetal Heart	heart
26	chr12:49741200-49742000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:49741200-49742200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:49741200-49742200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
29	chr12:49741200-49742200	Bivalent Enhancer	Ovary	ovary
30	chr12:49741200-49742400	Flanking Active TSS	NHLF	lung
31	chr12:49741400-49742000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:49741400-49742000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr12:49741400-49742000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr12:49741400-49742000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:49741400-49742000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:49741400-49742000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr12:49741400-49742000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
38	chr12:49741400-49742000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:49741400-49742000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:49741400-49742000	Bivalent Enhancer	Fetal Brain Male	brain
41	chr12:49741400-49742000	Active TSS	Gastric	stomach
42	chr12:49741400-49742000	Enhancers	Left Ventricle	heart
43	chr12:49741400-49742000	Active TSS	A549	lung
44	chr12:49741400-49742000	Flanking Active TSS	HUVEC	blood vessel
45	chr12:49741400-49742200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr12:49741400-49742200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:49741400-49742200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:49741400-49742200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
49	chr12:49741400-49742600	Active TSS	Fetal Kidney	kidney
50	chr12:49741400-49742600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum

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