Variant report

Variant	rs539527642
Chromosome Location	chr12:1099660-1099661
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	GATA2	chr12:1098921-1100285	SH-SY5Y	brain:	n/a	n/a
2	TAF1	chr12:1099494-1100331	Hela-S3	cervix:	n/a	n/a
3	MXI1	chr12:1098997-1100330	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:1098467-1101358	MCF10A-Er-Src	breast:	n/a	n/a
5	ZNF384	chr12:1099442-1099691	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:1098800-1100528	PBDE	blood:	n/a	n/a
7	CREB1	chr12:1099558-1100748	H1-hESC	embryonic stem cell:	n/a	n/a
8	RCOR1	chr12:1099580-1100256	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:1099401-1100668	HL-60	blood:	n/a	n/a
10	REST	chr12:1099554-1100283	SK-N-SH	brain:	n/a	chr12:1099819-1099839
11	CTCF	chr12:1099520-1099670	HEEpiC	esophagus:	n/a	n/a
12	POLR2A	chr12:1099536-1100370	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:1099520-1100681	A549	lung:	n/a	n/a
14	POLR2A	chr12:1099603-1100667	HepG2	liver:	n/a	n/a
15	HEY1	chr12:1099542-1100719	HepG2	liver:	n/a	chr12:1099901-1099916 chr12:1099952-1099967
16	POLR2A	chr12:1099607-1100649	GM19193	blood:	n/a	n/a
17	MTA3	chr12:1099513-1100322	GM12878	blood:	n/a	n/a
18	MXI1	chr12:1098625-1101473	IMR90	lung:	n/a	n/a
19	KAP1	chr12:1098803-1100210	U2OS	brain:	n/a	n/a
20	MAX	chr12:1099452-1100797	MCF-7	breast:	n/a	n/a
21	POLR2A	chr12:1099082-1100758	K562	blood:	n/a	n/a
22	E2F6	chr12:1099343-1100410	A549	lung:	n/a	chr12:1099599-1099609 chr12:1099811-1099820
23	CCNT2	chr12:1099598-1100750	K562	blood:	n/a	chr12:1099952-1099961 chr12:1100669-1100678 chr12:1100693-1100702
24	ZBTB33	chr12:1099552-1100280	A549	lung:	n/a	n/a
25	HEY1	chr12:1099533-1100334	K562	blood:	n/a	chr12:1099901-1099916 chr12:1099952-1099967
26	ZNF263	chr12:1098963-1100293	HEK293-T-REx	kidney:	n/a	n/a
27	POLR2A	chr12:1099490-1100644	K562	blood:	n/a	n/a
28	MAX	chr12:1099494-1100363	K562	blood:	n/a	n/a
29	RCOR1	chr12:1099655-1100546	HepG2	liver:	n/a	n/a
30	REST	chr12:1099411-1100663	HL-60	blood:	n/a	chr12:1099819-1099839 chr12:1100546-1100564 chr12:1100551-1100565
31	POLR2A	chr12:1099534-1100797	NB4	blood:	n/a	n/a
32	PAX5	chr12:1099654-1100301	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:1099470-1100684	HCT-116	colon:	n/a	n/a
34	ZBTB7A	chr12:1099455-1101225	ECC-1	luminal epithelium:	n/a	chr12:1100728-1100739
35	MYC	chr12:1099551-1100396	MCF-7	breast:	n/a	n/a
36	TAF1	chr12:1099462-1100586	PFSK-1	brain:	n/a	n/a
37	MYBL2	chr12:1099385-1100387	HepG2	liver:	n/a	n/a
38	TAF1	chr12:1099440-1100976	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr12:1098763-1100365	U87	brain:	n/a	n/a
40	NR3C1	chr12:1099520-1100907	A549	lung:	n/a	chr12:1099860-1099876 chr12:1099861-1099875 chr12:1099860-1099876
41	POLR2A	chr12:1099600-1100585	K562	blood:	n/a	n/a
42	POLR2A	chr12:1098769-1100359	U87	brain:	n/a	n/a
43	MYC	chr12:1099590-1100214	MCF-7	breast:	n/a	n/a
44	MAX	chr12:1098950-1100517	SK-N-SH	brain:	n/a	n/a
45	GATA3	chr12:1099392-1100580	A549	lung:	n/a	n/a
46	TBP	chr12:1099622-1100662	HepG2	liver:	n/a	n/a
47	TEAD4	chr12:1099487-1100825	ECC-1	luminal epithelium:	n/a	n/a
48	FOXP2	chr12:1099551-1100706	PFSK-1	brain:	n/a	n/a
49	TCF12	chr12:1099277-1100852	A549	lung:	n/a	n/a
50	EGR1	chr12:1099383-1100370	ECC-1	luminal epithelium:	n/a	chr12:1099697-1099707 chr12:1099695-1099710 chr12:1099697-1099707 chr12:1099696-1099709 chr12:1099697-1099706 chr12:1099696-1099709 chr12:1099693-1099707 chr12:1099696-1099709 chr12:1099697-1099708 chr12:1099695-1099709 chr12:1099691-1099713 chr12:1099697-1099708 chr12:1099696-1099709

No.	Distal block	Cell Line	Cell type
1	chr1:200638978..200639820-chr12:1099606..1100160,2	Hela-S3	cervix:
2	chr12:541135..544043-chr12:1097640..1100614,2	K562	blood:
3	chr12:1098483..1100095-chr12:1136049..1138258,2	K562	blood:
4	chr12:1099319..1102192-chr19:46282612..46285259,2	MCF-7	breast:
5	chr12:1058754..1060950-chr12:1097741..1100141,2	MCF-7	breast:
6	chr12:1099568..1100284-chr22:38597718..38598499,2	Hela-S3	cervix:
7	chr1:23885419..23886416-chr12:1099306..1100258,2	Hela-S3	cervix:
8	chr12:1056985..1060702-chr12:1098122..1101434,9	MCF-7	breast:
9	chr12:1099424..1099985-chr15:78857604..78858376,2	Hela-S3	cervix:
10	chr12:1097166..1102781-chr12:1103327..1109862,10	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NINJ2-2	chr12:1099221-1100283	NONHSAT025381
2	lnc-NINJ2-2	chr12:1099453-1099774	ENSG00000250132.2

Variant related genes	Relation type
ERC1	TF binding region
RAD52	TF binding region
ENSG00000250132	TF binding region
ENSG00000185022	Chromatin interaction
ENSG00000082805	Chromatin interaction
ENSG00000118197	Chromatin interaction
ENSG00000002016	Chromatin interaction
ENSG00000104936	Chromatin interaction
ENSG00000169684	Chromatin interaction
ENSG00000120647	Chromatin interaction
ENSG00000117318	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1052589	chr12:910460-1421493	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
11	nsv468960	chr12:975276-1455106	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv556941	chr12:975276-1455106	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv1044329	chr12:985144-1403020	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	nsv541340	chr12:985144-1403020	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv470256	chr12:998365-1438761	Enhancers Strong transcription Weak transcription ZNF genes & repeats 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv492321	chr12:1011692-1388512	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	nsv898579	chr12:1013176-1510505	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv898580	chr12:1024688-1569097	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
19	nsv1036488	chr12:1041097-1445923	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
20	nsv1037825	chr12:1045734-1432940	Bivalent/Poised TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	nsv541342	chr12:1045734-1432940	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
22	nsv868854	chr12:1045935-1354083	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
23	nsv468962	chr12:1047531-1119958	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
24	nsv556942	chr12:1047531-1119958	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
25	esv2762958	chr12:1049279-1554962	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
26	nsv1052559	chr12:1077964-1588543	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
27	nsv898581	chr12:1084783-1527359	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
28	nsv1041799	chr12:1091294-1304839	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
29	nsv541343	chr12:1091294-1304839	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
30	esv3357464	chr12:1099316-1101864	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 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	chr12:1097600-1099800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:1097600-1099800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:1097800-1099800	Flanking Active TSS	Dnd41	blood
4	chr12:1097800-1100000	Active TSS	Right Atrium	heart
5	chr12:1098000-1099800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:1098000-1099800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr12:1098000-1100000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr12:1098400-1100000	Flanking Active TSS	Osteobl	bone
9	chr12:1098600-1100200	Flanking Active TSS	HMEC	breast
10	chr12:1098600-1101200	Active TSS	Psoas Muscle	Psoas
11	chr12:1098600-1101600	Active TSS	Aorta	Aorta
12	chr12:1098600-1101800	Active TSS	Fetal Brain Male	brain
13	chr12:1098800-1099800	Flanking Active TSS	NH-A	brain
14	chr12:1098800-1101200	Active TSS	Ovary	ovary
15	chr12:1098800-1101400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr12:1098800-1101600	Active TSS	Left Ventricle	heart
17	chr12:1098800-1101600	Active TSS	Right Ventricle	heart
18	chr12:1098800-1101800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr12:1099000-1099800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr12:1099000-1100000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr12:1099000-1100000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr12:1099000-1101000	Active TSS	Fetal Brain Female	brain
23	chr12:1099000-1101200	Active TSS	Colonic Mucosa	Colon
24	chr12:1099000-1101200	Active TSS	Esophagus	oesophagus
25	chr12:1099000-1101200	Active TSS	Lung	lung
26	chr12:1099000-1101600	Active TSS	H9 Cell Line	embryonic stem cell
27	chr12:1099000-1101600	Active TSS	Fetal Muscle Trunk	muscle
28	chr12:1099000-1101800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:1099000-1101800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr12:1099200-1099800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr12:1099200-1099800	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr12:1099200-1099800	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr12:1099200-1099800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:1099200-1099800	Active TSS	Brain Germinal Matrix	brain
35	chr12:1099200-1099800	Bivalent/Poised TSS	HepG2	liver
36	chr12:1099200-1100200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:1099200-1101000	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr12:1099200-1101000	Active TSS	Stomach Mucosa	stomach
39	chr12:1099200-1101000	Active TSS	K562	blood
40	chr12:1099200-1101200	Active TSS	Brain Cingulate Gyrus	brain
41	chr12:1099200-1101200	Active TSS	Brain Hippocampus Middle	brain
42	chr12:1099200-1101200	Active TSS	Fetal Intestine Small	intestine
43	chr12:1099200-1101200	Active TSS	Fetal Stomach	stomach
44	chr12:1099200-1101200	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr12:1099200-1101200	Active TSS	Stomach Smooth Muscle	stomach
46	chr12:1099200-1101400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:1099200-1101400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:1099200-1101400	Active TSS	Colon Smooth Muscle	Colon
49	chr12:1099200-1101400	Active TSS	Fetal Intestine Large	intestine
50	chr12:1099200-1101600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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