Variant report

Variant	rs74089062
Chromosome Location	chr12:49742089-49742090
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	SP1	chr12:49741262-49742139	A549	lung:	n/a	chr12:49741868-49741882
2	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
3	ZBTB7A	chr12:49738646-49742163	ECC-1	luminal epithelium:	n/a	chr12:49739274-49739281 chr12:49741924-49741935 chr12:49741555-49741564
4	SP1	chr12:49741156-49742136	A549	lung:	n/a	chr12:49741189-49741202 chr12:49741868-49741882
5	EP300	chr12:49741306-49742392	A549	lung:	n/a	chr12:49742310-49742319 chr12:49741615-49741631 chr12:49742311-49742320
6	REST	chr12:49741010-49742198	A549	lung:	n/a	chr12:49741422-49741442 chr12:49741591-49741604 chr12:49741582-49741595
7	TAF1	chr12:49741383-49742195	A549	lung:	n/a	n/a
8	CTCF	chr12:49742020-49742170	GM12873	blood:	n/a	n/a
9	POLR2A	chr12:49741455-49742756	HepG2	liver:	n/a	n/a
10	SMC3	chr12:49740372-49742164	SK-N-SH	brain:	n/a	chr12:49741556-49741570 chr12:49741556-49741566 chr12:49741019-49741027
11	MBD4	chr12:49741559-49742094	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:49741512-49742143	MCF-7	breast:	n/a	n/a
13	CTCF	chr12:49741960-49742110	SK-N-SH_RA	brain:	n/a	n/a
14	POLR2A	chr12:49741384-49742095	HCT-116	colon:	n/a	n/a
15	SIX5	chr12:49741173-49742180	A549	lung:	n/a	n/a
16	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
17	MYBL2	chr12:49741287-49742324	HepG2	liver:	n/a	n/a
18	MAZ	chr12:49741247-49742527	IMR90	lung:	n/a	chr12:49742310-49742319 chr12:49742311-49742320
19	ELF1	chr12:49741380-49742113	A549	lung:	n/a	chr12:49741594-49741606 chr12:49741549-49741558
20	POLR2A	chr12:49741630-49742622	HepG2	liver:	n/a	n/a
21	HEY1	chr12:49741515-49742112	HepG2	liver:	n/a	n/a
22	MYBL2	chr12:49741259-49742102	HepG2	liver:	n/a	n/a
23	MAX	chr12:49740356-49742248	A549	lung:	n/a	n/a
24	CTCF	chr12:49742033-49742109	K562	blood:	n/a	n/a
25	ELF1	chr12:49741385-49742097	MCF-7	breast:	n/a	chr12:49741594-49741606 chr12:49741549-49741558
26	TCF12	chr12:49740483-49742251	A549	lung:	n/a	chr12:49741032-49741042 chr12:49742192-49742199
27	POLR2A	chr12:49741420-49742168	U87	brain:	n/a	n/a
28	POLR2A	chr12:49741060-49744599	K562	blood:	n/a	n/a

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

Variant related genes	Relation type
DNAJC22	TF binding region
ENSG00000123352	Chromatin interaction
ENSG00000199237	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000258284	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	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168981	0.94[ASN][1000 genomes]
rs11831313	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	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12310129	0.98[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12317856	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17123696	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1874909	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874910	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874911	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270741	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60331259	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60494978	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74089059	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49739000-49742200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr12:49739200-49742200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
3	chr12:49739400-49742200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:49739600-49742400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
5	chr12:49740200-49742200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:49740600-49742200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
7	chr12:49740600-49742200	Flanking Active TSS	Hela-S3	cervix
8	chr12:49740800-49742400	Flanking Active TSS	Pancreas	Pancrea
9	chr12:49741000-49742400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
10	chr12:49741000-49742600	Bivalent Enhancer	Fetal Heart	heart
11	chr12:49741200-49742200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:49741200-49742200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
13	chr12:49741200-49742200	Bivalent Enhancer	Ovary	ovary
14	chr12:49741200-49742400	Flanking Active TSS	NHLF	lung
15	chr12:49741400-49742200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:49741400-49742200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:49741400-49742200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:49741400-49742200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
19	chr12:49741400-49742600	Active TSS	Fetal Kidney	kidney
20	chr12:49741400-49742600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
21	chr12:49741600-49742200	Bivalent Enhancer	Primary B cells from cord blood	blood
22	chr12:49741600-49742200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr12:49741600-49742200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr12:49741600-49742200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
25	chr12:49741600-49742200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:49741600-49742200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:49741600-49742400	Active TSS	Liver	Liver
28	chr12:49741600-49742400	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr12:49741600-49742400	Flanking Active TSS	HSMM	muscle
30	chr12:49741600-49742400	Active TSS	HSMMtube	muscle
31	chr12:49741800-49742200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:49741800-49742200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
33	chr12:49741800-49742200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
34	chr12:49741800-49742200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:49741800-49742200	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr12:49741800-49742200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
37	chr12:49741800-49742200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
38	chr12:49741800-49742200	Bivalent Enhancer	Small Intestine	intestine
39	chr12:49741800-49742400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr12:49741800-49742400	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr12:49741800-49742400	Flanking Active TSS	NH-A	brain
42	chr12:49741800-49742600	Flanking Active TSS	Stomach Mucosa	stomach
43	chr12:49741800-49743000	Bivalent Enhancer	Placenta	Placenta
44	chr12:49741800-49743200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr12:49742000-49742200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
46	chr12:49742000-49742200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:49742000-49742200	Bivalent Enhancer	Adipose Nuclei	Adipose
48	chr12:49742000-49742200	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
49	chr12:49742000-49742200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:49742000-49742200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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