Variant report

Variant	rs1877484
Chromosome Location	chr12:122110770-122110771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr12:122110367-122110876	A549	lung:	n/a	n/a
2	CHD2	chr12:122110404-122110795	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:122110324-122110799	Raji	blood:	n/a	n/a
4	KAP1	chr12:122109797-122110835	HEK293	kidney:	n/a	n/a
5	MXI1	chr12:122109738-122111743	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr12:122110167-122110851	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:122110301-122110777	HUVEC	blood vessel:	n/a	n/a
8	CREB1	chr12:122110293-122110883	GM12878	blood:	n/a	n/a
9	CEBPB	chr12:122110568-122110783	Hela-S3	cervix:	n/a	n/a
10	ZEB1	chr12:122110100-122110826	HepG2	liver:	n/a	chr12:122110470-122110477 chr12:122110480-122110487
11	GABPA	chr12:122110198-122110916	SK-N-SH	brain:	n/a	n/a
12	RUNX3	chr12:122110721-122110976	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:122110325-122110772	SK-N-MC	brain:	n/a	n/a
14	NFATC1	chr12:122110231-122110772	GM12878	blood:	n/a	n/a
15	FOXA2	chr12:122110436-122110891	A549	lung:	n/a	n/a
16	POLR2A	chr12:122110607-122111367	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr12:122110343-122110808	GM12878	blood:	n/a	n/a
18	HA-E2F1	chr12:122110193-122110785	MCF-7	breast:	n/a	n/a
19	ELF1	chr12:122110262-122110869	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:122110180-122110782	H1-hESC	embryonic stem cell:	n/a	n/a
21	ELF1	chr12:122109956-122110838	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:122110111-122110809	HUVEC	blood vessel:	n/a	n/a
23	JUND	chr12:122109884-122110825	H1-hESC	embryonic stem cell:	n/a	n/a
24	MTA3	chr12:122109780-122110867	GM12878	blood:	n/a	n/a
25	CREB1	chr12:122110256-122110906	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr12:122110298-122110788	U87	brain:	n/a	n/a
27	POLR2A	chr12:122110181-122110837	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr12:122110359-122110920	PBDE	blood:	n/a	n/a
29	CREB1	chr12:122110455-122110824	A549	lung:	n/a	n/a
30	E2F4	chr12:122110436-122110811	GM12878	blood:	n/a	n/a
31	SIN3A	chr12:122110444-122110810	GM12878	blood:	n/a	n/a
32	GABPA	chr12:122110229-122111088	MCF-7	breast:	n/a	n/a
33	POLR2A	chr12:122110622-122110796	HepG2	liver:	n/a	n/a
34	POLR2A	chr12:122110578-122110820	Hela-S3	cervix:	n/a	n/a
35	GABPA	chr12:122110299-122110829	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr12:122110248-122110792	MCF-7	breast:	n/a	n/a
37	E2F4	chr12:122110380-122110801	MCF10A-Er-Src	breast:	n/a	n/a
38	GABPA	chr12:122110264-122111064	MCF-7	breast:	n/a	n/a
39	POLR2A	chr12:122110111-122110788	U87	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122062970..122066467-chr12:122109966..122112755,3	MCF-7	breast:
2	chr12:121986936..121988892-chr12:122109089..122111571,2	MCF-7	breast:
3	chr12:122063149..122066007-chr12:122110767..122112513,2	MCF-7	breast:

No data

Variant related genes	Relation type
MORN3	TF binding region
ENSG00000182500	Chromatin interaction
ENSG00000089094	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10743188	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10840652	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11043179	0.80[AFR][1000 genomes]
rs12320939	0.84[EUR][1000 genomes]
rs2309142	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2669163	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2669165	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2669166	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2669168	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2720021	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720022	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720025	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2720035	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2942368	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2942370	0.80[AMR][1000 genomes]
rs2942379	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2954116	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3825175	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6486789	0.84[EUR][1000 genomes]
rs7135617	0.85[EUR][1000 genomes]
rs7297028	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7397295	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7978609	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7978866	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	173 gene(s)	inside rSNPs	diseases
3	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122103200-122116000	Weak transcription	K562	blood
2	chr12:122109400-122111000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr12:122109400-122111200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr12:122109400-122111200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr12:122109800-122110800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:122109800-122110800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr12:122109800-122110800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:122109800-122111000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr12:122109800-122111000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr12:122109800-122111000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:122109800-122111000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:122109800-122111000	Active TSS	Brain Germinal Matrix	brain
13	chr12:122109800-122111000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:122109800-122111000	Active TSS	Fetal Kidney	kidney
15	chr12:122109800-122111000	Flanking Active TSS	Placenta	Placenta
16	chr12:122109800-122111000	Flanking Active TSS	GM12878-XiMat	blood
17	chr12:122109800-122111200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr12:122109800-122111200	Flanking Active TSS	Dnd41	blood
19	chr12:122109800-122111400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:122110000-122110800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:122110000-122110800	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr12:122110000-122110800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr12:122110000-122110800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:122110000-122110800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr12:122110000-122110800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:122110000-122110800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr12:122110000-122110800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:122110000-122110800	Flanking Active TSS	Fetal Brain Male	brain
29	chr12:122110000-122110800	Active TSS	Fetal Lung	lung
30	chr12:122110000-122110800	Active TSS	NHLF	lung
31	chr12:122110000-122111000	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr12:122110000-122111000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
33	chr12:122110000-122111000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:122110000-122111000	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr12:122110000-122111000	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr12:122110000-122111000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr12:122110000-122111000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr12:122110000-122111000	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr12:122110000-122111000	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr12:122110000-122111000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:122110000-122111000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr12:122110000-122111000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:122110000-122111000	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr12:122110000-122111000	Active TSS	Brain Hippocampus Middle	brain
45	chr12:122110000-122111000	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr12:122110000-122111000	Flanking Active TSS	Fetal Thymus	thymus
47	chr12:122110000-122111000	Active TSS	Rectal Smooth Muscle	rectum
48	chr12:122110000-122111000	Active TSS	Right Ventricle	heart
49	chr12:122110000-122111200	Flanking Active TSS	Colonic Mucosa	Colon
50	chr12:122110000-122111400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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