Variant report

Variant	rs73237255
Chromosome Location	chr12:9802742-9802743
allele	C/T
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	MXI1	chr12:9800287-9802771	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:9802742-9803720	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:9802705-9803122	GM12891	blood:	n/a	n/a
4	CHD1	chr12:9800337-9804156	GM12878	blood:	n/a	chr12:9800667-9800677 chr12:9800660-9800670
5	TBL1XR1	chr12:9799984-9802966	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:9799451-9804403	GM19193	blood:	n/a	n/a
7	MTA3	chr12:9799406-9804477	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:9799501-9804451	GM12891	blood:	n/a	n/a
9	MYC	chr12:9801820-9803973	MCF10A-Er-Src	breast:	n/a	chr12:9803552-9803562
10	POLR2A	chr12:9799408-9804409	GM19099	blood:	n/a	n/a
11	TBP	chr12:9802082-9802946	GM12878	blood:	n/a	n/a
12	UBTF	chr12:9801914-9802802	K562	blood:	n/a	n/a
13	POLR2A	chr12:9799328-9804610	GM12878	blood:	n/a	n/a
14	ATF2	chr12:9800087-9804473	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:9800142-9804355	GM18951	blood:	n/a	n/a
16	POLR2A	chr12:9799314-9804469	GM12892	blood:	n/a	n/a
17	POLR2A	chr12:9799782-9803691	NB4	blood:	n/a	n/a
18	NFIC	chr12:9799779-9804349	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:9802728-9803204	HL-60	blood:	n/a	n/a
20	POLR2A	chr12:9799501-9804422	GM18526	blood:	n/a	n/a
21	STAT5A	chr12:9799903-9804021	GM12878	blood:	n/a	chr12:9800489-9800496 chr12:9801700-9801711 chr12:9803497-9803505 chr12:9800768-9800780
22	POLR2A	chr12:9799475-9804347	GM12892	blood:	n/a	n/a
23	RELA	chr12:9800358-9802939	GM18526	blood:	n/a	n/a
24	POLR2A	chr12:9799681-9804387	Raji	blood:	n/a	n/a
25	NFIC	chr12:9800239-9802953	GM12878	blood:	n/a	n/a
26	RELA	chr12:9799625-9804451	GM19193	blood:	n/a	n/a
27	RELA	chr12:9799837-9804323	GM18505	blood:	n/a	n/a
28	POLR2A	chr12:9802455-9802787	K562	blood:	n/a	n/a
29	POLR2A	chr12:9800204-9803221	HL-60	blood:	n/a	n/a
30	BCLAF1	chr12:9799795-9803076	GM12878	blood:	n/a	chr12:9800683-9800696 chr12:9800565-9800578
31	RELA	chr12:9799841-9804488	GM18951	blood:	n/a	n/a
32	POLR2A	chr12:9799734-9803978	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr12:9799520-9804579	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:9799517-9804360	GM12878	blood:	n/a	n/a
35	RUNX3	chr12:9802733-9804441	GM12878	blood:	n/a	chr12:9803476-9803491
36	POLR2A	chr12:9799348-9804458	GM12892	blood:	n/a	n/a
37	POLR2A	chr12:9800379-9802983	GM10847	blood:	n/a	n/a
38	POLR2A	chr12:9802739-9802758	GM12878	blood:	n/a	n/a
39	FOXM1	chr12:9801921-9802932	GM12878	blood:	n/a	n/a
40	PML	chr12:9800165-9804429	GM12878	blood:	n/a	chr12:9800521-9800529 chr12:9802383-9802391
41	POLR2A	chr12:9799943-9804384	GM15510	blood:	n/a	n/a
42	RELA	chr12:9800185-9802970	GM19099	blood:	n/a	n/a
43	POLR2A	chr12:9801756-9804395	GM12892	blood:	n/a	n/a
44	RELA	chr12:9801973-9804409	GM15510	blood:	n/a	n/a
45	POLR2A	chr12:9799739-9804357	GM18505	blood:	n/a	n/a
46	POLR2A	chr12:9802678-9803762	GM12891	blood:	n/a	n/a
47	POLR2A	chr12:9800105-9803897	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr12:9802731-9803709	HepG2	liver:	n/a	n/a
49	IKZF1	chr12:9800290-9804161	GM12878	blood:	n/a	n/a
50	MTA3	chr12:9802665-9803203	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9801303..9803979-chr12:9875830..9877610,2	K562	blood:
2	chr12:9799292..9802850-chr12:9823422..9827161,3	MCF-7	breast:
3	chr12:9801031..9803712-chr12:9946954..9949811,3	K562	blood:
4	chr12:9739995..9741756-chr12:9800822..9803051,2	K562	blood:
5	chr12:9800923..9803675-chr12:9838767..9841892,3	MCF-7	breast:
6	chr12:9800782..9802831-chr12:9859086..9861954,2	MCF-7	breast:
7	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:
8	chr12:9600285..9602561-chr12:9801026..9803503,2	K562	blood:
9	chr12:9800783..9805047-chr12:9809567..9813940,5	K562	blood:
10	chr12:9786143..9793024-chr12:9797652..9803573,13	MCF-7	breast:
11	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256594	TF binding region
ENSG00000256442	TF binding region
ENSG00000069493	Chromatin interaction
ENSG00000214826	Chromatin interaction
ENSG00000256594	Chromatin interaction
ENSG00000257027	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10732553	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734805	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771997	0.86[EUR][1000 genomes]
rs10771999	0.94[EUR][1000 genomes]
rs1108452	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108453	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17732859	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4439599	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488098	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488100	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306991	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316769	1.00[EUR][1000 genomes];1.00[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	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9799800-9803600	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr12:9800000-9802800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:9800000-9802800	Active TSS	Fetal Kidney	kidney
4	chr12:9800000-9803400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:9800000-9803600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:9800000-9804000	Active TSS	Rectal Smooth Muscle	rectum
7	chr12:9800200-9802800	Active TSS	NHDF-Ad	bronchial
8	chr12:9800200-9803400	Active TSS	Brain Anterior Caudate	brain
9	chr12:9800200-9803400	Active TSS	Esophagus	oesophagus
10	chr12:9800200-9803400	Active TSS	Right Ventricle	heart
11	chr12:9800200-9803400	Active TSS	HSMMtube	muscle
12	chr12:9800200-9803600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:9800200-9804000	Active TSS	Right Atrium	heart
14	chr12:9800400-9802800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:9800400-9802800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:9800400-9803200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:9800400-9803400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:9800400-9803400	Active TSS	Brain Hippocampus Middle	brain
19	chr12:9800400-9803600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:9800400-9803600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr12:9800400-9803600	Active TSS	K562	blood
22	chr12:9800400-9803800	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr12:9800600-9802800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:9800600-9802800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:9800600-9802800	Active TSS	HSMM	muscle
26	chr12:9800600-9803000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:9800600-9803000	Active TSS	Primary B cells from peripheral blood	blood
28	chr12:9800600-9803000	Active TSS	Stomach Smooth Muscle	stomach
29	chr12:9800600-9803000	Active TSS	GM12878-XiMat	blood
30	chr12:9800600-9803400	Active TSS	Colonic Mucosa	Colon
31	chr12:9800600-9803400	Active TSS	Fetal Thymus	thymus
32	chr12:9800600-9803400	Active TSS	NHLF	lung
33	chr12:9800600-9803600	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr12:9800600-9803600	Active TSS	Primary T cells from cord blood	blood
35	chr12:9800600-9803600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:9800600-9803600	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr12:9800600-9803600	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr12:9800600-9803600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:9800600-9803600	Active TSS	Thymus	Thymus
40	chr12:9800600-9803600	Active TSS	Monocytes-CD14+_RO01746	blood
41	chr12:9800600-9803800	Active TSS	Primary T cells fromperipheralblood	blood
42	chr12:9800600-9803800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:9800600-9804000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr12:9800600-9804200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:9800800-9803800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:9801000-9803000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr12:9801000-9803200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
48	chr12:9801000-9803200	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr12:9801000-9803400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:9801000-9804400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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