Variant report

Variant	rs67133230
Chromosome Location	chr12:46124413-46124414
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	chr12:46124288-46124416	Gliobla	brain:	n/a	n/a
2	TAF1	chr12:46124182-46124667	GM12878	blood:	n/a	n/a
3	CTCF	chr12:46124340-46124490	Caco-2	colon:	n/a	chr12:46124420-46124433
4	POLR2A	chr12:46124158-46124615	H1-hESC	embryonic stem cell:	n/a	n/a
5	HA-E2F1	chr12:46123957-46124447	Hela-S3	cervix:	n/a	chr12:46124071-46124080
6	YY1	chr12:46124230-46124669	SK-N-SH	brain:	n/a	chr12:46124295-46124306 chr12:46124495-46124507
7	POLR2A	chr12:46124179-46124651	Hela-S3	cervix:	n/a	n/a
8	TAF1	chr12:46124160-46124607	H1-hESC	embryonic stem cell:	n/a	n/a
9	ELK1	chr12:46124378-46124487	Hela-S3	cervix:	n/a	n/a
10	EP300	chr12:46124385-46124516	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:46122122-46124616	K562	blood:	n/a	n/a
12	YY1	chr12:46124122-46124691	GM12878	blood:	n/a	chr12:46124295-46124306 chr12:46124495-46124507
13	MAFK	chr12:46124361-46124523	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr12:46124278-46125037	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:46124271-46124971	HepG2	liver:	n/a	n/a
16	ARID3A	chr12:46124352-46125041	HepG2	liver:	n/a	n/a
17	CHD2	chr12:46124330-46124534	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr12:46124186-46124673	K562	blood:	n/a	n/a
19	RUNX3	chr12:46124250-46124636	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:46124201-46124554	MCF-7	breast:	n/a	n/a
21	POLR2A	chr12:46120616-46124553	GM18951	blood:	n/a	n/a
22	TBP	chr12:46124297-46125419	H1-hESC	embryonic stem cell:	n/a	n/a
23	CUX1	chr12:46124312-46125061	K562	blood:	n/a	chr12:46124870-46124879 chr12:46124868-46124877 chr12:46124868-46124877 chr12:46124731-46124742
24	TAF1	chr12:46124151-46124598	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr12:46124180-46124597	GM12878	blood:	n/a	n/a
26	TBP	chr12:46124349-46125219	Hela-S3	cervix:	n/a	n/a
27	HEY1	chr12:46124227-46124431	K562	blood:	n/a	n/a
28	MAZ	chr12:46122230-46124648	K562	blood:	n/a	chr12:46122927-46122937
29	HCFC1	chr12:46124371-46124557	K562	blood:	n/a	n/a
30	POLR2A	chr12:46120645-46124550	GM19099	blood:	n/a	n/a
31	TBL1XR1	chr12:46124409-46124600	GM12878	blood:	n/a	n/a
32	UBTF	chr12:46122338-46124713	K562	blood:	n/a	n/a
33	GATA3	chr12:46124178-46124700	T-47D	breast:	n/a	chr12:46124283-46124290
34	POLR2A	chr12:46124185-46124609	HCT-116	colon:	n/a	n/a
35	MAX	chr12:46124266-46124526	Hela-S3	cervix:	n/a	n/a
36	E2F4	chr12:46123596-46124529	MCF10A-Er-Src	breast:	n/a	chr12:46123763-46123775 chr12:46124071-46124080
37	POLR2A	chr12:46124194-46124521	GM12878	blood:	n/a	n/a
38	YY1	chr12:46124214-46124614	K562	blood:	n/a	chr12:46124295-46124306 chr12:46124495-46124507
39	TAF1	chr12:46122050-46124761	ECC-1	luminal epithelium:	n/a	n/a
40	STAT3	chr12:46124347-46124508	MCF10A-Er-Src	breast:	n/a	n/a
41	SIN3AK20	chr12:46122239-46124686	MCF-7	breast:	n/a	n/a
42	TCF7L2	chr12:46124188-46124836	HCT-116	colon:	n/a	n/a
43	POLR2A	chr12:46124265-46124515	Hela-S3	cervix:	n/a	n/a
44	IRF1	chr12:46124357-46124546	K562	blood:	n/a	n/a
45	POLR2A	chr12:46123444-46124596	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr12:46124151-46124565	GM12878	blood:	n/a	n/a
47	MAX	chr12:46124075-46125011	A549	lung:	n/a	n/a
48	POLR2A	chr12:46124260-46124538	GM12892	blood:	n/a	n/a
49	TAF1	chr12:46124306-46124542	GM12892	blood:	n/a	n/a
50	GATA2	chr12:46124393-46125030	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46122734..46124564-chr12:46660289..46662102,2	K562	blood:
2	chr12:46119690..46125014-chr12:46381902..46386942,12	K562	blood:
3	chr12:46123074..46125001-chr12:46284357..46286236,2	K562	blood:
4	chr12:45608238..45611148-chr12:46119877..46124655,5	K562	blood:
5	chr12:45609285..45610968-chr12:46122757..46125582,2	K562	blood:
6	chr12:46122058..46125027-chr12:46229101..46230947,2	K562	blood:
7	chr12:46119117..46128831-chr12:46378175..46388065,20	MCF-7	breast:
8	chr12:46117578..46127110-chr12:46379884..46387671,22	K562	blood:
9	chr12:45749106..45751356-chr12:46123739..46125901,2	MCF-7	breast:
10	chr12:46121418..46125188-chr12:46383049..46386096,7	MCF-7	breast:

Variant related genes	Relation type
LINC00938	TF binding region
ENSG00000134297	Chromatin interaction
ENSG00000139218	Chromatin interaction
ENSG00000189079	Chromatin interaction
ENSG00000111371	Chromatin interaction
ENSG00000177119	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10748432	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10880855	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10880859	0.86[EUR][1000 genomes]
rs10880860	0.84[EUR][1000 genomes]
rs11183201	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12319077	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12320533	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1468993	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1863127	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2059404	0.83[EUR][1000 genomes]
rs2193749	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2408435	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs247930	0.80[EUR][1000 genomes]
rs35115	0.80[EUR][1000 genomes]
rs35117	0.80[EUR][1000 genomes]
rs6582574	0.85[EUR][1000 genomes]
rs7132422	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7138997	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7955891	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7976870	0.81[AMR][1000 genomes];0.81[EUR][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	nsv899052	chr12:46068394-46175469	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
2	nsv899053	chr12:46100053-46141372	Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
3	esv3515708	chr12:46121785-46125883	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	49 gene(s)	inside rSNPs	diseases
4	esv3515709	chr12:46121785-46125883	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	49 gene(s)	inside rSNPs	diseases
5	esv3421413	chr12:46122210-46125058	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	46 gene(s)	inside rSNPs	diseases
6	esv3398512	chr12:46122335-46125333	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region	46 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	chr12:46116600-46127200	Active TSS	GM12878-XiMat	blood
2	chr12:46117800-46126600	Active TSS	Fetal Thymus	thymus
3	chr12:46118000-46127000	Active TSS	Thymus	Thymus
4	chr12:46118400-46125000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr12:46118400-46126000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:46118400-46126000	Active TSS	NHLF	lung
7	chr12:46118600-46125000	Active TSS	Dnd41	blood
8	chr12:46118600-46125000	Active TSS	K562	blood
9	chr12:46118600-46125200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:46118600-46126000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:46118800-46125200	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr12:46118800-46125600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:46118800-46126000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:46118800-46126400	Active TSS	Fetal Muscle Leg	muscle
15	chr12:46118800-46127200	Active TSS	Ovary	ovary
16	chr12:46119000-46125400	Active TSS	Brain Angular Gyrus	brain
17	chr12:46119000-46125400	Active TSS	Fetal Muscle Trunk	muscle
18	chr12:46119000-46125800	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr12:46119000-46126000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:46119000-46126200	Active TSS	H1 Cell Line	embryonic stem cell
21	chr12:46119000-46126200	Active TSS	Brain Germinal Matrix	brain
22	chr12:46119000-46126400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:46119000-46126400	Active TSS	Aorta	Aorta
24	chr12:46119000-46126400	Active TSS	Fetal Stomach	stomach
25	chr12:46119000-46126400	Active TSS	Right Ventricle	heart
26	chr12:46119000-46126800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr12:46119000-46127000	Active TSS	Psoas Muscle	Psoas
28	chr12:46119200-46124800	Active TSS	Brain Cingulate Gyrus	brain
29	chr12:46119200-46124800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:46119200-46125000	Active TSS	Brain Anterior Caudate	brain
31	chr12:46119200-46125000	Active TSS	Brain Hippocampus Middle	brain
32	chr12:46119200-46125000	Active TSS	Duodenum Mucosa	Duodenum
33	chr12:46119200-46125200	Active TSS	NH-A	brain
34	chr12:46119200-46125400	Active TSS	Colon Smooth Muscle	Colon
35	chr12:46119200-46125400	Active TSS	HSMM	muscle
36	chr12:46119200-46125600	Active TSS	Fetal Kidney	kidney
37	chr12:46119200-46125800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:46119200-46125800	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr12:46119200-46126000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:46119200-46126000	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr12:46119200-46126200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:46119200-46126200	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr12:46119200-46126600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:46119200-46126800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:46119200-46126800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:46119200-46127000	Active TSS	Primary T cells fromperipheralblood	blood
47	chr12:46119200-46127400	Active TSS	Stomach Smooth Muscle	stomach
48	chr12:46119400-46125000	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr12:46119400-46125000	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr12:46119400-46125200	Active TSS	Fetal Intestine Small	intestine

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