Variant report

Variant	rs535560028
Chromosome Location	chr12:124458708-124458709
allele	A/C
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	TAF1	chr12:124458457-124458759	SK-N-SH	brain:	n/a	n/a
2	YY1	chr12:124456965-124458720	HepG2	liver:	n/a	chr12:124458606-124458620 chr12:124457859-124457873 chr12:124457388-124457397 chr12:124457455-124457466 chr12:124457391-124457400 chr12:124458387-124458398 chr12:124457081-124457095 chr12:124457080-124457089 chr12:124457719-124457730 chr12:124457394-124457403 chr12:124457075-124457089 chr12:124457858-124457872 chr12:124457950-124457964 chr12:124457389-124457403
3	RUNX3	chr12:124458302-124458742	GM12878	blood:	n/a	n/a
4	REST	chr12:124458318-124458804	ECC-1	luminal epithelium:	n/a	chr12:124458758-124458766 chr12:124458339-124458352 chr12:124458582-124458591
5	MAZ	chr12:124455899-124458832	IMR90	lung:	n/a	chr12:124457562-124457572 chr12:124457558-124457568 chr12:124457947-124457957 chr12:124457536-124457545 chr12:124457385-124457395
6	GTF2F1	chr12:124458492-124458885	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr12:124458560-124458710	HAc	cerebellar:	n/a	n/a
8	REST	chr12:124458394-124458792	PFSK-1	brain:	n/a	chr12:124458758-124458766 chr12:124458582-124458591
9	TAF1	chr12:124458394-124458774	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr12:124458267-124458782	MCF-7	breast:	n/a	n/a
11	BHLHE40	chr12:124458549-124458726	K562	blood:	n/a	chr12:124458574-124458590
12	REST	chr12:124458394-124458760	K562	blood:	n/a	chr12:124458582-124458591
13	RUNX3	chr12:124458288-124458800	GM12878	blood:	n/a	n/a
14	MXI1	chr12:124455887-124459788	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr12:124458560-124458710	GM12874	blood:	n/a	n/a
16	UBTF	chr12:124456240-124458968	K562	blood:	n/a	n/a
17	YY1	chr12:124458147-124458736	H1-hESC	embryonic stem cell:	n/a	chr12:124458606-124458620 chr12:124458387-124458398
18	CTCF	chr12:124457078-124458791	SK-N-SH	brain:	n/a	chr12:124457429-124457445
19	REST	chr12:124458409-124458764	HepG2	liver:	n/a	chr12:124458582-124458591
20	MAX	chr12:124456967-124458825	A549	lung:	n/a	chr12:124457562-124457572 chr12:124457558-124457568 chr12:124457947-124457957 chr12:124457536-124457545 chr12:124457385-124457395
21	WRNIP1	chr12:124458600-124458722	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:124456819-124458721	Hela-S3	cervix:	n/a	n/a
23	YY1	chr12:124457884-124458752	GM12892	blood:	n/a	chr12:124458606-124458620 chr12:124458387-124458398 chr12:124457950-124457964
24	CTCF	chr12:124458640-124458790	A549	lung:	n/a	n/a
25	REST	chr12:124455987-124459250	H1-neurons	neurons:	n/a	chr12:124458758-124458766 chr12:124458339-124458352 chr12:124457841-124457854 chr12:124456713-124456733 chr12:124458582-124458591 chr12:124457610-124457620
26	MAZ	chr12:124456939-124458755	K562	blood:	n/a	chr12:124457562-124457572 chr12:124457558-124457568 chr12:124457947-124457957 chr12:124457536-124457545 chr12:124457385-124457395
27	REST	chr12:124458375-124458834	HCT-116	colon:	n/a	chr12:124458758-124458766 chr12:124458582-124458591
28	POLR2A	chr12:124458384-124458796	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZNF143	chr12:124458447-124458738	GM12878	blood:	n/a	n/a
30	YY1	chr12:124458041-124458750	ECC-1	luminal epithelium:	n/a	chr12:124458606-124458620 chr12:124458387-124458398
31	UBTF	chr12:124458143-124458897	K562	blood:	n/a	n/a
32	MAFK	chr12:124458500-124458783	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr12:124458560-124458710	GM12867	blood:	n/a	n/a
34	RCOR1	chr12:124458403-124458770	K562	blood:	n/a	n/a
35	ZEB1	chr12:124458425-124458724	GM12878	blood:	n/a	n/a
36	REST	chr12:124458300-124458833	PFSK-1	brain:	n/a	chr12:124458758-124458766 chr12:124458339-124458352 chr12:124458582-124458591
37	MXI1	chr12:124458453-124458724	Hela-S3	cervix:	n/a	n/a
38	REST	chr12:124458437-124458724	Hela-S3	cervix:	n/a	chr12:124458582-124458591
39	CHD1	chr12:124458249-124458876	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:124458654-124458747	Hela-S3	cervix:	n/a	n/a
41	ZNF143	chr12:124458522-124458782	H1-hESC	embryonic stem cell:	n/a	n/a
42	MTA3	chr12:124458349-124458822	GM12878	blood:	n/a	n/a
43	YY1	chr12:124458143-124458775	ECC-1	luminal epithelium:	n/a	chr12:124458606-124458620 chr12:124458387-124458398
44	EGR1	chr12:124458427-124458760	K562	blood:	n/a	chr12:124458607-124458618 chr12:124458603-124458617 chr12:124458607-124458617
45	POLR2A	chr12:124456681-124458733	MCF-7	breast:	n/a	n/a
46	CTCF	chr12:124458347-124458732	K562	blood:	n/a	n/a
47	REST	chr12:124458403-124458716	GM12878	blood:	n/a	chr12:124458582-124458591
48	SMC3	chr12:124458559-124458739	Hela-S3	cervix:	n/a	n/a
49	JUND	chr12:124458453-124458739	K562	blood:	n/a	n/a
50	EGR1	chr12:124458503-124458732	GM12878	blood:	n/a	chr12:124458607-124458618 chr12:124458603-124458617 chr12:124458607-124458617

No.	Distal block	Cell Line	Cell type
1	chr12:124117230..124119880-chr12:124454893..124459230,4	K562	blood:
2	chr12:124442245..124448648-chr12:124455013..124459797,7	K562	blood:
3	chr12:124443831..124448109-chr12:124456314..124459797,5	K562	blood:
4	chr12:124137852..124140530-chr12:124458317..124460698,2	K562	blood:
5	chr12:124450327..124455412-chr12:124455418..124460730,10	K562	blood:
6	chr12:124116659..124120709-chr12:124455290..124460616,5	K562	blood:
7	chr12:124456565..124458963-chr17:72427263..72429561,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270061	TF binding region
ENSG00000270095	TF binding region
CCDC92	TF binding region
ENSG00000269997	Chromatin interaction
ENSG00000270130	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000270048	Chromatin interaction
ENSG00000170412	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000269938	Chromatin interaction
ENSG00000270061	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3404000	chr12:124455199-124459397	Active TSS Enhancers Flanking Active TSS Weak transcription 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	21 gene(s)	inside rSNPs	diseases
3	esv3338195	chr12:124456524-124459372	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
4	esv3493374	chr12:124458433-124496012	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv3493363	chr12:124458497-124495976	Strong transcription Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv3493385	chr12:124458565-124495928	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124454600-124459800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:124455200-124459000	Active TSS	NHDF-Ad	bronchial
3	chr12:124455600-124458800	Active TSS	HMEC	breast
4	chr12:124455600-124459000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:124455600-124459400	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr12:124455600-124459400	Active TSS	Fetal Intestine Large	intestine
7	chr12:124455800-124458800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:124455800-124458800	Active TSS	Brain Angular Gyrus	brain
9	chr12:124455800-124458800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:124455800-124459000	Active TSS	Fetal Intestine Small	intestine
11	chr12:124456000-124458800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:124456000-124458800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:124456000-124458800	Active TSS	Aorta	Aorta
14	chr12:124456000-124458800	Active TSS	A549	lung
15	chr12:124456000-124458800	Active TSS	GM12878-XiMat	blood
16	chr12:124456000-124458800	Active TSS	HSMM	muscle
17	chr12:124456000-124458800	Active TSS	NH-A	brain
18	chr12:124456000-124459000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr12:124456000-124459000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr12:124456000-124459000	Active TSS	Left Ventricle	heart
21	chr12:124456000-124459000	Active TSS	Right Ventricle	heart
22	chr12:124456000-124459200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:124456000-124459200	Active TSS	Brain Cingulate Gyrus	brain
24	chr12:124456000-124459200	Active TSS	Duodenum Mucosa	Duodenum
25	chr12:124456000-124459400	Active TSS	NHLF	lung
26	chr12:124456200-124458800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:124456200-124458800	Active TSS	Small Intestine	intestine
28	chr12:124456200-124459000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:124456200-124459000	Active TSS	Esophagus	oesophagus
30	chr12:124456200-124459000	Active TSS	Gastric	stomach
31	chr12:124456200-124459000	Active TSS	Lung	lung
32	chr12:124456200-124459000	Active TSS	Ovary	ovary
33	chr12:124456200-124459000	Active TSS	Pancreas	Pancrea
34	chr12:124456200-124459000	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr12:124456200-124459200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:124456400-124458800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:124456400-124459000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:124456400-124459000	Active TSS	HSMMtube	muscle
39	chr12:124456400-124459200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:124456600-124458800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:124456600-124458800	Active TSS	Hela-S3	cervix
42	chr12:124456600-124458800	Active TSS	K562	blood
43	chr12:124456600-124459000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:124456600-124459000	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr12:124456600-124459000	Active TSS	Placenta Amnion	Placenta Amnion
46	chr12:124456800-124459400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:124457000-124459200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:124457800-124458800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
49	chr12:124457800-124458800	Active TSS	Fetal Lung	lung
50	chr12:124457800-124459200	Active TSS	Fetal Kidney	kidney

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