Variant report

Variant	rs550723261
Chromosome Location	chr12:57854080-57854081
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	chr12:57852528-57856905	A549	lung:	n/a	chr12:57855088-57855100 chr12:57854788-57854797 chr12:57855421-57855430 chr12:57854019-57854032 chr12:57856662-57856671 chr12:57855543-57855552 chr12:57855232-57855244 chr12:57855089-57855099 chr12:57855429-57855443 chr12:57855571-57855580 chr12:57854556-57854565 chr12:57855541-57855553 chr12:57853860-57853872 chr12:57854024-57854036 chr12:57855089-57855098 chr12:57855570-57855582 chr12:57856000-57856009 chr12:57853899-57853911 chr12:57854788-57854797 chr12:57855233-57855247 chr12:57856151-57856163 chr12:57856152-57856161 chr12:57855594-57855608 chr12:57855090-57855099 chr12:57855547-57855561 chr12:57856000-57856014 chr12:57855999-57856011 chr12:57853861-57853871 chr12:57854546-57854560 chr12:57855232-57855244 chr12:57853861-57853870 chr12:57855570-57855582 chr12:57856152-57856166 chr12:57853659-57853668 chr12:57855567-57855581 chr12:57855572-57855581 chr12:57855542-57855551 chr12:57853154-57853161 chr12:57854024-57854036 chr12:57856153-57856162 chr12:57855090-57855099 chr12:57856001-57856010 chr12:57855085-57855099 chr12:57856525-57856539 chr12:57856151-57856163 chr12:57854788-57854798 chr12:57855999-57856011 chr12:57854025-57854034 chr12:57853836-57853850 chr12:57856152-57856162 chr12:57855232-57855243 chr12:57854021-57854035 chr12:57855114-57855127 chr12:57853901-57853910 chr12:57855089-57855099 chr12:57855088-57855100 chr12:57855950-57855964 chr12:57856000-57856010 chr12:57855543-57855552 chr12:57854557-57854566
2	EP300	chr12:57853991-57854750	A549	lung:	n/a	chr12:57854554-57854570 chr12:57854167-57854181
3	CTCF	chr12:57853855-57857058	A549	lung:	n/a	chr12:57856610-57856631 chr12:57854445-57854463 chr12:57854447-57854468 chr12:57854448-57854457 chr12:57856617-57856630 chr12:57854448-57854461 chr12:57856579-57856592 chr12:57856615-57856633
4	SIN3AK20	chr12:57854008-57854755	A549	lung:	n/a	n/a
5	JUND	chr12:57852674-57854161	A549	lung:	n/a	chr12:57853993-57854002 chr12:57853903-57853912
6	TCF12	chr12:57852429-57856996	A549	lung:	n/a	chr12:57854335-57854342 chr12:57856056-57856063
7	SP1	chr12:57852535-57856861	A549	lung:	n/a	chr12:57855088-57855100 chr12:57854788-57854797 chr12:57855421-57855430 chr12:57854019-57854032 chr12:57856662-57856671 chr12:57855543-57855552 chr12:57855232-57855244 chr12:57855089-57855099 chr12:57855429-57855443 chr12:57855571-57855580 chr12:57854556-57854565 chr12:57855541-57855553 chr12:57853860-57853872 chr12:57854024-57854036 chr12:57855089-57855098 chr12:57855570-57855582 chr12:57856000-57856009 chr12:57853899-57853911 chr12:57854788-57854797 chr12:57855233-57855247 chr12:57856151-57856163 chr12:57856152-57856161 chr12:57855594-57855608 chr12:57855090-57855099 chr12:57855547-57855561 chr12:57856000-57856014 chr12:57855999-57856011 chr12:57853861-57853871 chr12:57854546-57854560 chr12:57855232-57855244 chr12:57853861-57853870 chr12:57855570-57855582 chr12:57856152-57856166 chr12:57853659-57853668 chr12:57855567-57855581 chr12:57855572-57855581 chr12:57855542-57855551 chr12:57853154-57853161 chr12:57854024-57854036 chr12:57856153-57856162 chr12:57855090-57855099 chr12:57856001-57856010 chr12:57855085-57855099 chr12:57856525-57856539 chr12:57856151-57856163 chr12:57854788-57854798 chr12:57855999-57856011 chr12:57854025-57854034 chr12:57853836-57853850 chr12:57856152-57856162 chr12:57855232-57855243 chr12:57854021-57854035 chr12:57855114-57855127 chr12:57853901-57853910 chr12:57855089-57855099 chr12:57855088-57855100 chr12:57855950-57855964 chr12:57856000-57856010 chr12:57855543-57855552 chr12:57854557-57854566
8	REST	chr12:57854020-57854620	A549	lung:	n/a	chr12:57854567-57854580 chr12:57854572-57854581
9	RUNX3	chr12:57854080-57854443	GM12878	blood:	n/a	n/a
10	GATA3	chr12:57852767-57856918	A549	lung:	n/a	chr12:57853695-57853706 chr12:57856399-57856409 chr12:57855281-57855292
11	BCL3	chr12:57853897-57856889	A549	lung:	n/a	chr12:57855572-57855581 chr12:57854572-57854581 chr12:57854557-57854566 chr12:57856000-57856009 chr12:57855538-57855551
12	NR2F2	chr12:57854075-57854806	K562	blood:	n/a	n/a
13	MAX	chr12:57852555-57854782	A549	lung:	n/a	chr12:57854560-57854570
14	ZBTB7A	chr12:57852573-57856893	ECC-1	luminal epithelium:	n/a	n/a
15	ZBTB7A	chr12:57852281-57856952	ECC-1	luminal epithelium:	n/a	n/a
16	SIN3A	chr12:57852690-57856788	H1-hESC	embryonic stem cell:	n/a	chr12:57856650-57856663 chr12:57854571-57854581 chr12:57854567-57854580 chr12:57854738-57854749 chr12:57853962-57853975 chr12:57855427-57855438
17	MAZ	chr12:57852515-57854465	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57852621..57854513-chr12:58130296..58131944,2	K562	blood:
2	chr12:57849885..57859254-chr12:57908711..57915821,16	K562	blood:
3	chr12:57848732..57851043-chr12:57853897..57856236,2	MCF-7	breast:
4	chr12:57822750..57826133-chr12:57852904..57855936,4	K562	blood:
5	chr12:57693773..57695685-chr12:57852034..57854514,2	K562	blood:
6	chr12:57852034..57858739-chr12:57911478..57917144,8	MCF-7	breast:
7	chr12:57853636..57856322-chr12:58144624..58147677,3	K562	blood:
8	chr12:57633619..57639143-chr12:57853203..57857806,7	K562	blood:
9	chr12:57852892..57855767-chr12:58158814..58160402,2	K562	blood:
10	chr12:57853636..57856322-chr12:58144624..58146178,2	K562	blood:
11	chr12:57851728..57854572-chr12:58144859..58146430,2	MCF-7	breast:
12	chr12:57820715..57827591-chr12:57847165..57857509,18	K562	blood:
13	chr12:57850154..57858218-chr12:57910899..57919538,20	K562	blood:

Variant related genes	Relation type
GLI1	TF binding region
ENSG00000185633	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000258001	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv8974	chr12:57852779-57865881	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57852400-57854600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr12:57852400-57856600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:57852400-57856800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:57852600-57854200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr12:57852600-57854200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:57852600-57854600	Active TSS	Psoas Muscle	Psoas
7	chr12:57852600-57856600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr12:57852600-57856600	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr12:57852800-57854200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:57852800-57854200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:57852800-57854200	Active TSS	Primary T cells from cord blood	blood
12	chr12:57852800-57854200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:57852800-57854400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr12:57852800-57854400	Active TSS	Ovary	ovary
15	chr12:57852800-57854400	Active TSS	Small Intestine	intestine
16	chr12:57852800-57854600	Active TSS	Left Ventricle	heart
17	chr12:57852800-57854800	Active TSS	Right Atrium	heart
18	chr12:57852800-57856400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr12:57852800-57856600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr12:57852800-57856600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:57852800-57856600	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr12:57852800-57856600	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr12:57852800-57856600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:57852800-57856600	Active TSS	Aorta	Aorta
25	chr12:57853000-57854200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:57853000-57854200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:57853000-57854200	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr12:57853000-57854200	Active TSS	Brain Cingulate Gyrus	brain
29	chr12:57853000-57854200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:57853000-57854200	Active TSS	Colon Smooth Muscle	Colon
31	chr12:57853000-57854200	Active TSS	Fetal Brain Female	brain
32	chr12:57853000-57854200	Active TSS	Fetal Intestine Large	intestine
33	chr12:57853000-57854200	Active TSS	Fetal Lung	lung
34	chr12:57853000-57854200	Active TSS	Fetal Stomach	stomach
35	chr12:57853000-57854200	Active TSS	GM12878-XiMat	blood
36	chr12:57853000-57854200	Active TSS	HepG2	liver
37	chr12:57853000-57854400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:57853000-57854400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:57853000-57854400	Active TSS	Rectal Smooth Muscle	rectum
40	chr12:57853000-57854600	Active TSS	Right Ventricle	heart
41	chr12:57853000-57856600	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr12:57853000-57856600	Active TSS	A549	lung
43	chr12:57853000-57856800	Active TSS	Brain Substantia Nigra	brain
44	chr12:57853000-57856800	Active TSS	Fetal Kidney	kidney
45	chr12:57853200-57854200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:57853200-57854400	Active TSS	Colonic Mucosa	Colon
47	chr12:57853400-57854200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr12:57853400-57854200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:57853400-57854200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:57853400-57854200	Active TSS	Breast Myoepithelial Primary Cells	Breast

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